SubtiWiki - User contributions [en]

YqxD

2010-11-08T17:07:40Z

Jourde: past immediate neighbour "dnaG" changed to "antE"

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yqxD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 7.172
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 588 bp, 196 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[antE]]'', ''[[yqfL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14452]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqxD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25230

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqxD-dnaG-sigA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10312]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0178 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/P17868 P17868]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25230]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yqxD]]-[[dnaG]]-[[sigA]]'' {{PubMed|3298998}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|3298998}}, [[SigB]]{{PubMed|10411753}}, [[SigH]] {{PubMed|3127379}}

* '''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>3298998 10411753 3127379</pubmed>
[[Category:Protein-coding genes]]

YqxD

2010-11-08T17:06:55Z

Jourde: Undo revision 129000 by Jourde (talk)

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yqxD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 7.172
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 588 bp, 196 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaG]]'', ''[[yqfL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14452]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqxD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25230

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqxD-dnaG-sigA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10312]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0178 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/P17868 P17868]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25230]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yqxD]]-[[dnaG]]-[[sigA]]'' {{PubMed|3298998}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|3298998}}, [[SigB]]{{PubMed|10411753}}, [[SigH]] {{PubMed|3127379}}

* '''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>3298998 10411753 3127379</pubmed>
[[Category:Protein-coding genes]]

YqxD

2010-11-08T17:06:27Z

Jourde: past immediate neighbour "dnaG" changed to "antE"

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yqxD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 7.172
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 588 bp, 196 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaG]]'', ''[[antE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14452]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yqxD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25230

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqxD-dnaG-sigA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10312]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' UPF0178 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/P17868 P17868]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25230]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yqxD]]-[[dnaG]]-[[sigA]]'' {{PubMed|3298998}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|3298998}}, [[SigB]]{{PubMed|10411753}}, [[SigH]] {{PubMed|3127379}}

* '''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>3298998 10411753 3127379</pubmed>
[[Category:Protein-coding genes]]

AntE

2010-11-08T17:05:34Z

Jourde: immediate neighbours "sigA" and "dnaG" changed to "dnaG" and "yqxD" respectivly

* '''Description:''' ''[[dnaG]]'' overlapping gene of unknown function 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''antE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 10.718
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 294 bp, 98 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaG]]'', ''[[yqxD]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/antE_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/antE_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:antE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25220

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14178]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q7WY63 Q7WY63]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25220]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[antE]]'' {{PubMed|9864351}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|9864351}}

* '''Regulation:'''

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>9864351,20817675, </pubmed>

[[Category:Protein-coding genes]]

DnaG

2010-11-08T17:04:29Z

Jourde: immediate neighbours "antE" and "yqxD" changed to "sigA" and "antE" respectivly

* '''Description:''' DNA primase, part of the [[replisome]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''dnaG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaE ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA primase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 68 kDa, 6.706
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1809 bp, 603 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sigA]]'', ''[[antE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14451]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:dnaG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25210

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqxD-dnaG-sigA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10313]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:''' the enzymatic activity is inhibited by (p)ppGpp during the ´stringent response´ {{PubMed|17350574}}

* '''Interactions:''' part of the [[replisome]]: [[PolC]]-[[HolA]]-[[HolB]]-[[DnaX]]-[[DnaN]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[SsbA]]-[[DnaE]]-[[PriA]]-[[DnaB]] {{PubMed|20122408}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1D0Q 1D0Q] (zinc binding domain, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=1Z8S 1Z8S] (DnaB binding domain, AA 452-597, Geobacillus stearothermophilus)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P05096 P05096]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25210]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yqxD]]-[[dnaG]]-[[sigA]]'' {{PubMed|3298998}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|3298998}}, [[SigB]]{{PubMed|10411753}}, [[SigH]] {{PubMed|3127379}}

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
** enzymatic activity is inhibited by (p)ppGpp during the ´stringent response´

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

* '''Additional information:'''
** enzymatic activity is inhibited by (p)ppGpp during the ´stringent response´ {{PubMed|17350574}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>3919021, 20122408,14651647, 16479537, 19415803 17350574 </pubmed>

[[Category:Protein-coding genes]]

SigA

2010-11-08T17:03:09Z

Jourde: next immediate neighbour "antE" changed to "dnaG"

* '''Description:''' [[RNA polymerase]] major [[sigma factor]] SigA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoD, crsA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] major [[sigma factor]] SigA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || transcription
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 4.634
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1113 bp, 371 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cccA]]'', ''[[dnaG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14450]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:sigA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU25200

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqxD-dnaG-sigA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10314]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''[[Genes controlled by SigA|List of SigA controlled genes]]'''

* '''Protein family:''' sigma-70 factor family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[Spo0A]]-[[SigA]] {{PubMed|14976210}}, [[SigA]]-([[RpoB]]-[[RpoC]]) {{PubMed|19680289,19735077}}

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P06224 P06224]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25200]

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

=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[yqxD]]-[[dnaG]]-[[sigA]]'' {{PubMed|3298998}}
** ''[[sigA]]'' {{PubMed|3919021}}

* '''[[Sigma factor]]:'''
** ''[[yqxD]]'': [[SigA]] {{PubMed|3298998}}, [[SigB]]{{PubMed|10411753}}, [[SigH]] {{PubMed|3127379}}
** ''[[sigA]]'': [[SigD]] {{PubMed|3919021}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

* [[Charles Moran]], Emory University, NC, USA [http://www.microbiology.emory.edu/moran_c.html homepage]

=Your additional remarks=

=References=
<pubmed> 12486038,10556308,8107087, 14762002,7918363,8071196,7630711,9185571,9287022, 14679239, 14976210 19735077, 2997585,9658000,3127379 10438769,11535782,7599136, 9144176 19680289</pubmed>

Additional publication: {{PubMed|20935043,20817769}}
[[Category:Protein-coding genes]]

NrdEB

2010-11-08T15:16:56Z

Jourde: past immediate neighbour "yosP" changed to "yosQ"

* '''Description:''' similar to ribonucleoside-diphosphate reductase (alpha subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''nrdEB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yosN ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 6.388
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3504 bp, 1084 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yosQ]]'', ''[[yosM]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13898]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yosN_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU20060

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13723]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== 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/O31875 O31875]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU20060]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 11470879 16621400 9465078</pubmed>
[[Category:Protein-coding genes]]

YosP

2010-11-08T15:15:19Z

Jourde: immediate neighbours "yosQ" and "nrdEB" changed to "yosR" and "yosQ" respectivly

* '''Description:''' similar to ribonucleoside-diphosphate reductase (beta subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yosP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''nrdF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 6.094
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1795 bp, 329 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yosR]]'', ''[[yosQ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13896]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yosP_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU20040

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13725]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== 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/O30601 O30601]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU20040]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 11470879 16621400 9465078</pubmed>
[[Category:Protein-coding genes]]

YosQ

2010-11-08T15:13:13Z

Jourde: immediate neighbours "yosR" and "yosP" changed to "yosP" and "nrdEB" respectivly

* '''Description:''' similar to phage-related endodeoxyribonuclease 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yosQ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 10.196
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 519 bp, 173 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yosP]]'', ''[[nrdEB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13895]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yosQ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU20050

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13726]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34479 O34479]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU20050]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YosR

2010-11-08T15:11:43Z

Jourde: next immediate neighbour "yosQ" changed to "yosP"

* '''Description:''' similar to thioredoxin 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yosR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 8 kDa, 4.379
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 240 bp, 80 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yosS]]'', ''[[yosP]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13894]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yosR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU20030

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13727]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' Bacterial-type thyA subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34342 O34342]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU20030]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YeeA

2010-11-08T09:38:08Z

Jourde: past immediate neighbour "yefB" changed to "yefC"

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yeeA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 100 kDa, 5.674
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2637 bp, 879 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yefC]]'', ''[[yeeB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12496]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yeeA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU06760

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12818]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31504 O31504]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06760]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

EbrA

2010-11-08T09:35:21Z

Jourde: next immediate neighbour "ymaF" changed to "ymaG"

* '''Description:''' multidrug efflux transporter 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ebrA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || multidrug efflux transporter
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || multidrug resistance
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 9.373
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 315 bp, 105 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ebrB]]'', ''[[ymaG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13614]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ebrA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU17300

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12585]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[EbrA]]-[[EbrB]] {{PubMed|17417881}}

* '''Localization:''' cell membrane {{PubMed|17417881}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31792 O31792]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17300]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>17417881 </pubmed>
[[Category:Protein-coding genes]]

MiaA

2010-11-08T09:34:09Z

Jourde: past immediate neighbour "ymaG" changed to "ymaF"

* '''Description:''' tRNA isopentenylpyrophosphate transferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''miaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || tRNA isopentenylpyrophosphate transferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 6.002
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 942 bp, 314 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ymaF]]'', ''[[hfq]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13617]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:miaA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU17330

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12617]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Isopentenyl diphosphate + tRNA = diphosphate + tRNA containing 6-isopentenyladenosine (according to Swiss-Prot)

* '''Protein family:''' IPP transferase 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/O31795 O31795]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17330]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.5.1.8 2.5.1.8]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==The corresponding gene/ protein in other bacteria==
<pubmed> 11160115 3045085 9294434 </pubmed>
[[Category:Protein-coding genes]]

YmaG

2010-11-08T09:32:17Z

Jourde: immediate neighbours "ymaF" and "miaA" changed to "ebrA" and "ymaF" respectivly

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

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ymaG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || spore coat protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 9.679
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 369 bp, 123 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ebrA]]'', ''[[ymaF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13615]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ymaG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU17310

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13415]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:''' inner spore coat {{PubMed|19933362}}

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31793 O31793]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17310]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''ymaG'' {{PubMed|12480901}}

* '''[[Sigma factor]]:''' [[SigK]] {{PubMed|15699190,12480901}}

* '''Regulation:'''
** expressed late during sporulation in the mother cell ([[SigK]]) {{PubMed|15699190,12480901}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 15699190,12480901 19933362 </pubmed>
[[Category:Protein-coding genes]]

YmaF

2010-11-08T09:30:04Z

Jourde: immediate neighbours "ebrA" and "ymaG" changed to "ymaG" and "miaA" respectivly

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ymaF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 15 kDa, 6.363
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 411 bp, 137 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ymaG]]'', ''[[miaA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13616]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ymaF_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU17320

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13414]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31794 O31794]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17320]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>16479537 </pubmed>

[[Category:Protein-coding genes]]

YefC

2010-11-05T15:01:38Z

Jourde: immediate neighbours "yefA" and "yefB" changed to "yefB" and "yeeA" respectivly

* '''Description:''' similar to resolvase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yefC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 9.819
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yefB]]'', ''[[yeeA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12495]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yefC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU06750

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12828]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' site-specific recombinase resolvase 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/O35034 O35034]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06750]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YefB

2010-11-05T15:00:14Z

Jourde: immediate neighbours "yefC" and "yeeA" changed to "yefA" and "yefC" respectivly

* '''Description:''' similar to site-specific recombinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yefB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 9.298
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yefA]]'', ''[[yefC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12494]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yefB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU06740

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12827]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34574 O34574]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06740]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

RlmCD

2010-11-05T14:57:53Z

Jourde: next immediate neighbour "yefC" changed to "yefB"

* '''Description:''' similar to RNA methyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yefA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yerS ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 5.707
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1377 bp, 459 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dgkB]]'', ''[[yefB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12493]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yefA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU06730

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12826]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== 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/O31503 O31503]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06730]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

RocG

2009-12-07T12:29:14Z

Jourde:

* '''Description:''' [[trigger enzymes|trigger enzyme]]: catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''rocG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[trigger enzymes|trigger enzyme]]: glutamate dehydrogenase (major)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine utilization, controls the activity of [[GltC]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46.2 kDa, 6.28
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1272 bp, 424 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocA]]'', ''[[yweA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15806]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:rocG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37790

===Phenotypes of a mutant ===

Poor growth on complex media such as SP (sporulation medium). No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants ([[gudB |''gudB1'']])

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10621]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' L-glutamate + H2O + NAD+ = 2-oxoglutarate + NH3 + NADH (according to Swiss-Prot) L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the [[GltC]] transcription activator [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]

* '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family (according to Swiss-Prot) Glu/Leu/Phe/Val dehydrogenases family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' RocG-[[GltC]], this interaction prevents transcription activation of the ''[[gltA]]-[[gltB]]'' operon by GltC [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/search/structidSearch.do?structureId=3K92 3K92] (super-repressor mutant that is capable of constitutive inactivation of [[GltC]], E93K mutation)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39633 P39633]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37790]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2 1.4.1.2] 1.4.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''rocG''

* '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]

* '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]), ornithine or proline, subject to carbon catabolite repression ([[CcpA]])

* '''Regulatory mechanism:''' [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]; [[AhrC]]: transcription activation ; [[CcpA]]: transcription repression

* '''Additional information:'''
Activation by [[RocR]] requires binding of RocG to a downstream element [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]

=Biological materials =

* '''Mutant:''' GP747 (spc), GP726 (aphA3), GP810 (tet) available in [[Stülke]] lab

* '''Expression vector:'''
** expression of native ''rocG'' in ''B. subtilis'': pGP529 (in [[pBQ200]]), available in [[Stülke]] lab
** for purification of RocG carrying an N-terminal Strep-tag: pGP902 (in [[pGP172]]), a series of ''rocG'' variants is also available in [[pGP172]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

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

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=

'''Enzymatic activity of RocG'''
<pubmed>18603778,,16244435 16195607 ,18326565, 9829940 </pubmed>

'''Function in the control of [[GltC]] activity'''
<pubmed>15150225,17994626 ,17608797 17183217 </pubmed>

'''Expression of ''rocG'''''
<pubmed>12634342,15150224 10468601 9829940 </pubmed>

'''Structural analysis of glutamate dehydrogenase'''
<pubmed>8263917 </pubmed>

[[Category:Protein-coding genes]]

FbaA

2009-12-07T12:27:59Z

Jourde:

* '''Description:''' fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fbaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywjH]]'', ''[[spo0F]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15729]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:fbaA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37120

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate (according to Swiss-Prot)

* '''Protein family:''' class II fructose-bisphosphate aldolase family (according to Swiss-Prot)
* '''Paralogous protein(s):''' [[FbaB]]

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Domains:'''
** 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)

* '''Modification:''' phosphorylation on Thr-212 and Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):''' Zn2+ (Metalloenzyme)

* '''Effectors of protein activity:'''
** Inhibited by alpha-ketoglutarate, oxaloacetate and pyruvate [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P13243 P13243]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.13 4.1.2.13]

=== Additional information===

Binds 2 zinc ions per subunit. One is catalytic and the other provides a structural contribution

=Expression and regulation=

* '''Operon:'''
**''fbaA'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
**''fbaA-[[ywjH]]'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP88, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP395, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP601 (in [[pAC6]])

* '''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>17218307, 15125960, 24624 </pubmed>

[[Category:Protein-coding genes]]

YwdD

2009-12-07T12:21:26Z

Jourde:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywdD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-54d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 9.969
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 489 bp, 163 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywdE]]'', ''[[ywdC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15826]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ywdD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU38000

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10600]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39612 P39612]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38000]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YwdE

2009-12-07T12:20:58Z

Jourde:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywdE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipa-55d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 7.58
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 531 bp, 177 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywdF]]'', ''[[ywdD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15825]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ywdE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37990

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10601]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39613 P39613]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37990]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

Upp

2009-12-07T10:49:59Z

Jourde:

* '''Description:''' uracil phosphoribosyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''upp''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipc-35d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || uracil phosphoribosyltransferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || UMP synthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/pyrimidines_metabolism.html Pyrimidines], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.863
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 627 bp, 209 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[atpI]]'', ''[[glyA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/upp_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/upp_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:upp_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36890

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10945]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate (according to Swiss-Prot)

* '''Protein family:''' UPRTase 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/P39149 P39149]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36890]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.4.2.9 2.4.2.9]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>,7798145, </pubmed>

[[Category:Protein-coding genes]]

Crh

2009-12-07T10:30:05Z

Jourde:

* '''Description:''' "Catabolite repression [[HPr]]-like protein", Cofactor of the [[CcpA]] transcription factor 

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

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34740

===Phenotypes of a mutant ===

=== Database entries ===

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

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

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' [[HPr]] family (according to Swiss-Prot) [[PtsH]], [[HPr]] family

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

=== Extended information on the protein ===

* '''Kinetic information:'''

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

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

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

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

* '''Interactions:''' Crh-[[GapA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed], Crh-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 PubMed], [[HprK]]-Crh [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]

* '''Localization:'''

=== Database entries ===

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

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

=== Additional information===

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

=Expression and regulation=

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

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

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

* '''Regulatory mechanism:'''

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

=Biological materials =

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

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

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

* '''GFP fusion:'''

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

* '''Antibody:''' available in [[Stülke]] lab (not very good)

=Labs working on this gene/protein=

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

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

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

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

=Your additional remarks=

=References=

<pubmed>12972249 9973552 9237995 16272399 15126459 10217795 17142398 16316990, </pubmed>

[[Category:Protein-coding genes]]

CggR

2009-12-07T10:14:40Z

Jourde:

* '''Description:''' repressor of the glycolytic ''[[gapA]]'' operon, [[DeoR family]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cggR''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvbQ ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || central glycolytic genes regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional regulator
|-
|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''' || 37,2 kDa,5.68
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1020 bp, 340 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gapA]]'', ''[[araE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15400]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:cggR_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33950

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14085]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription repression of the glycolytic ''[[gapA]]'' operon

* '''Protein family:''' sorC transcriptional regulatory family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** DNA binding domain (H-T-H motif) (37–56)

* '''Modification:'''

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

* '''Effectors of protein activity:''' fructose 1.6-bisphosphate [http://www.ncbi.nlm.nih.gov/sites/entrez/12622823 PubMed] and dihydroxyacetone phosphate, glucose-6-phosphate and fructose-6-phosphate [http://www.ncbi.nlm.nih.gov/sites/entrez/18554327 PubMed] act as inducer and result in release of CggR from the DNA

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2OKG 2OKG] ( effector binding domain), [http://www.rcsb.org/pdb/explore.do?structureId=3BXH 3BXH] (in complex with fructose-6-phosphate), complex with Fructose-6-Phosphate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=65242 NCBI], effector binding domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=44226 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32253 O32253]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33950]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[cggR]]-[[gapA]]'' {{PubMed|11489127}}

The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. {{PubMed|11489127}} The processing event requires the [[Rny]] protein.

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (77-fold) ([[CggR]]) {{PubMed|12850135,12622823}}

* '''Regulatory mechanism:'''
** [[CggR]]: transcription repression {{PubMed|11489127}}

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP311 (in frame deletion), available in [[Stülke]] lab

* '''Expression vector:''' pGP705 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab

* '''lacZ fusion:''' pGP504 (in [[pAC7]]), pGP509 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

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

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=

<pubmed>19193632,12850135,12622823,18186488,10799476,11489127,12123463,12634343, 18554327, 18052209 , 17293407</pubmed>

[[Category:Protein-coding genes]]

GapA

2009-12-07T10:14:01Z

Jourde:

* '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|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''' || 35.7 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[cggR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15399]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:gapA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33940

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH (according to Swiss-Prot)
** This reaction is part of the glycolysis.

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''

* '''Modification:'''
** Phosphorylation on (Ser-148 OR Ser-151 OR Thr-153 OR Thr-154) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed1], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed2]
** Reversible thiol modifications after exposure to toxic quinones [http://www.ncbi.nlm.nih.gov/sites/entrez/18673455 PubMed]

* '''Cofactor(s):''' NAD+ (do not accept NADP+) [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

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

* '''Interactions:'''
** GapA-[[PtsH]]: [[PtsH|HPr(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
** GapA-[[Crh]]: [[Crh|Crh(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed], loosely membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1GD1 1GD1] (from ''Geobacillus stearothermophilus'')
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NQO 1NQO] (from ''Geobacillus stearothermophilus'', mutant with cys 149 replaced by ser, complex with NAD+ und D-Glyceraldehyde-3-Phosphate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09124 P09124]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33940]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.12 1.2.1.12]

=== Additional information===

GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]). Moreover, mutations in ''gapA'' from ''B. subtilis'' can suppress mutations in genes involved in DNA replication ([http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]).

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[cggR]]-[[gapA]]'' {{PubMed|11489127}}

The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. {{PubMed|11489127}} The processing event requires the [[Rny]] protein.

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (10 fold) ([[CggR]]) {{PubMed|12850135,12622823}}

* '''Regulatory mechanism:'''
** [[CggR]]: transcription repression {{PubMed|11489127}}

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]

* '''Additional information:''' GapA is one of the most abundant proteins in the cell. In the presence of glucose, there are about 25,000 GapA molecules per cell ([http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]).

=Biological materials =

* '''Mutant:''' essential, GM1501 (under p(spac) control), available in [[Stephane Aymerich]] lab

* '''Expression vector:'''
** pGP90 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)

* '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)

* '''GFP fusion:'''

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

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

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

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

=Your additional remarks=

=References=

<pubmed> 12850135,19193632, 18673455 , 17726680,16479537,12622823,12359717,10799476,17505547,11489127,12123463,17218307,12634343,17142398,17114254,10559165 </pubmed>

[[Category:Protein-coding genes]]

Pgk

2009-12-07T10:13:31Z

Jourde:

* '''Description:''' phosphoglycerate kinase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgk''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglycerate kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|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''' || 42,0 kDa, 4.77
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1182 bp, 394 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tpi]]'', ''[[gapA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15398]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pgk_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33930

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11062]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + 3-phospho-D-glycerate = ADP + 1,3-bisphosphoglycerate (according to Swiss-Prot)

* '''Protein family:''' phosphoglycerate kinase family (according to Swiss-Prot)
* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Two Substrate Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/7154941 PubMed]

* '''Domains:'''
** nucleotide binding domain (ATP) (350–353)
** 2x substrate binding domain (21–23), (59–62)

* '''Modification:''' phosphorylation on Ser-183 AND Thr-299 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+ or Mn2+ [http://www.ncbi.nlm.nih.gov/pubmed/7154941 PubMed]

* '''Effectors of protein activity:'''
** Inhibited by Co2+, NDP and NMP [http://www.ncbi.nlm.nih.gov/pubmed/7154941 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1PHP 1PHP] (Geobacillus stearothermophilus), ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=57113 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P40924 P40924]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33930]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.2.3 2.7.2.3]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP699 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1102 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP95 (N-terminal Strep-tag, in [[pGP172]]), available in [[Stülke]] lab
** pGP91 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]), available in [[Stülke]] lab
** pGP1513 (expression in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:''' pGP514 (in [[pAC6]]), a series of promoter deletion variants is also available in [[pAC6]], available in [[Stülke]] lab

* '''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> 16479537, 12850135 , 17726680, 11489127 ,17505547 , 17218307 7154941 </pubmed>

[[Category:Protein-coding genes]]

Tpi

2009-12-07T10:12:55Z

Jourde:

* '''Description:''' triose phosphate isomerase, glycolytic/ gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tpi''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tpiA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || triosephosphate isomerase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26,9 kDa, 4.79
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgm]]'', ''[[pgk]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15397]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:tpi_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33920

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10897]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-213 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:''' inhibited by 2-phosphoglycolate (in ''B. stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/8580851 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1BTM 1BTM] (complex with 2-phosphoglycolic acid, Geobacillus stearothermophilus), complex with 2-phosphpoglycolic acid, ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=48255 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P27876 P27876]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33920]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.1 5.3.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP700 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP394 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP89 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis), available in [[Stülke]] lab
** pGP1511 (expression in ''B. subtilis'', in [[pBQ200]]), 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:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 11489127 17505547 8021172 17218307 8580851 </pubmed>

[[Category:Protein-coding genes]]

Pgm

2009-12-07T10:12:19Z

Jourde:

* '''Description:''' phosphoglycerate mutase, glycolytic / gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgm''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gpmI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis / gluconeogenesis
|-
|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''' || 56,1 kDa, 5.21
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[eno]]'', ''[[tpi]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15396]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pgm_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33910

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10898]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = 3-phospho-D-glycerate (according to Swiss-Prot)

* '''Protein family:''' BPG-independent phosphoglycerate mutase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/33963 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-62 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mn2+

* '''Effectors of protein activity:'''
** Inhibited by diverse divalent heavy-metal ions, EDTA and 2,3-butanedione [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]
** 2,3-Diphosphoglycerate has NO role on this enzyme regulation [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]

* '''Interactions:''' Pgm-[[PfkA]]

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EJJ 1EJJ] (Geobacillus stearothermophilus, complex with 3-phosphoglycerate), [http://www.rcsb.org/pdb/explore.do?structureId=1EQJ 1EQJ] (Geobacillus stearothermophilus, complex with 2-phosphoglycerate), ''Geobacillus stearothermophilus'', complex with 2-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=16359 NCBI], ''Geobacillus stearothermophilus'', complex with 3-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=15578 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39773 P39773]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33910]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.1 5.4.2.1]]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP698 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1101 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP92 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), available in [[Stülke]] lab
** pGP1500 (expression in ''B. subtilis'', in [[pBQ200]]), 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:'''

=Labs working on this gene/protein=

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

[[Jedrzejas|Mark J. Jedrzejas]], Research Center Oakland, CA, USA [http://www.chori.org/Principal_Investigators/Jedrzejas_Mark_J/jedrzejas_research.html Homepage]

=Your additional remarks=

=References=

<pubmed>11514674,17085493,10764795,8215434,10747010,11712498,9830105,10388626,8636019,11827481,16479537, 12850135,17726680,17505547, 8021172,11489127, 10388626,10747010, 10764795, 11712498, 12729763, 17085493, 17218307 33963 </pubmed>

[[Category:Protein-coding genes]]

Eno

2009-12-07T10:11:35Z

Jourde:

* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''eno''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|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''' || 46,4 kDa, 4.49
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbK]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15395]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:eno_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33900

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H2O (according to Swiss-Prot) 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Domains:'''
** substrate binding domain (366–369)

* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by EDTA [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]

* '''Interactions:''' [[Eno]]-[[PfkA]], [[Eno]]-[[Rny]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] and membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3ES8 3ES8] (from ''Oceanobacillus iheyensis'', complex with Mg(2+) and malate)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37869 P37869]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11 4.2.1.11]

=== Additional information===
* Enolase is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
* There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
* [[universally conserved protein]]

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}

* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}

* '''Regulation:'''
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
** ''[[pgk]]'': constitutive {{PubMed|11489127}}

* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP698 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP563 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
** pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
** pGP1500 (expression in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab

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

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

=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> 17726680, 17218307, 12850135 , 19193632 , 11489127, 8021172, 17505547, 25885 </pubmed>

[[Category:Protein-coding genes]]

SigL

2009-12-07T10:06:32Z

Jourde:

* '''Description:''' Sigma subunit of the RNA polymerase, Sigma-54, Sigma L 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigL''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase sigma-54 factor (sigma-L)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of arginin, acetoin and fructose, required for cold adaptation
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49,5 kDa, 7.79
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1308 bp, 436 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvfH]]'', ''[[yvfG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15425]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sigL_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34200

===Phenotypes of a mutant ===

The mutant is cold-sensitive and unable to use arginine as a single carbon source. [http://www.ncbi.nlm.nih.gov/sites/entrez/16585774 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10748]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Binding to promoters of the -12, -24 type

* '''Protein family:''' sigma-54 factor family (according to Swiss-Prot) sigma-54 factor family

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

=== Genes/ operons controlled by SigL ===
''[[acoA]]-[[acoB]]-[[acoC]]-[[acoL]]'', ''[[rocA]]-[[rocB]]-[[rocC]]'', ''[[rocD]]-[[rocE]]-[[rocF]]'', ''[[rocG]]'', ''[[levD]]-[[levE]]-[[levF]]-[[levG]]-[[sacC]]'', ''[[ptb]]-[[bcd]]-[[buk]]-[[lpdV]]-[[bkdAA]]-[[bkdAB]]-[[bkdB]]''

===[[Transcription factors activating transcription at SigL-dependent promoters]]===
[[AcoR]], [[BkdR]], [[LevR]], [[RocR]], [[YplP]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** DNA binding domain (H-T-H motif) (324–343)
** pron box domain (413–421)
** 3 x Compositional bias domain (6–21),(32–53),(112–136)

* '''Modification:'''

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

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

* '''Interactions:''' [[SigL]]-[[AcoR]], [[SigL]]-[[RocR]], [[SigL]]-[[LevR]], [[SigL]]-[[BkdR]], [[SigL]]-[[YplP]], SigL-[[RpoB]]-[[RpoC]]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P24219 P24219]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34200]

=== Additional information===
Transcription initiation by SigL-containing RNA polymerase requires the activity of ATP-hydrolyzing transcription activators.

[[Transcription factors activating transcription at SigL-dependent promoters]]

=Expression and regulation=

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

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

* '''Regulation:''' repressed by glucose ([[CcpA]]) {{PubMed|16166551}}

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, transcriptional roadblock {{PubMed|16166551}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP146 (aphA3), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:'''

=Labs working on this gene/protein=

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

=Your additional remarks=

=References=

<pubmed>16585774,11274109,1924373 ,16166551 </pubmed>

[[Category:Protein-coding genes]]

YvrHa

2009-12-07T09:30:33Z

Jourde:

* '''Description:''' co-[[sigma factor]] (with [[YvrI]]) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yvrHa''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' rsoA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || write here
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || co-[[sigma factor]] (with [[YvrI]])
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA polymerase [[sigma factor]]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9.5 kDa, 4.69
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 240 bp, 79 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvrHb]]'', ''[[yvrI]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:YvrHa_yvrHb_context.GIF]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' does not exist

=== Additional information===

The sequence of the former ''yvrH'' gene was corrected, and does now contain two genes, ''[[yvrHa]]'' and ''[[yvrHb]]''.

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' corresponds to region 2 of a [[sigma factor]] {{PubMed|19940246}}

* '''Modification:'''

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

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

* '''Interactions:''' [[YvrHa]]-[[RpoC]] {{PubMed|19940246}}, [[YvrI]]-[[YvrHa]] {{PubMed|19940246}}

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/C0H3R4 C0H3R4]

* '''KEGG entry:''' no entry

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yvrI]]-[[yvrHa]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]

* '''[[Sigma factor]]:''' [[YvrI]]-[[YvrHa]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]

* '''Regulation:''' induced by acidic growth conditions [http://www.ncbi.nlm.nih.gov/sites/entrez/19047353 PubMed]

* '''Regulatory mechanism:''' activated by [[YvrHb]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]

=Your additional remarks=

=References=

<pubmed>18573182, 19940246,19047353,19047353, </pubmed>

[[Category:Protein-coding genes]]

YvrHb

2009-12-07T09:29:42Z

Jourde:

* '''Description:''' [[two-component systems|two-component]] response regulator 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yvrHb''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvrH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation cell surface maintenance
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26.6 kDa, 5.23
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 237 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvrG]]'', ''[[yvrHa]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:YvrHa_yvrHb_context.GIF]]
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

unusual autolysis and higher susceptibility to cell envelope antibiotics (bacitracin, aztreonam, cefepime, fosfomycin) [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' no entry

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcription activator [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]

* '''Protein family:''' OmpR family

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

=== The YvrHb regulon ===

subject to positive control: ''[[dltA]]-[[dltB]]-[[dltC]]-[[dltD]]-[[dltE]], [[sigX]]-[[rsiX]], [[sunA]], [[sunT]]-[[bdbA]]-[[yolJ]]-[[bdbB]], [[wapA]]-[[yxxG]], [[wprA]], [[yvrI]]-[[yvrHa]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]

subject to negative control: ''[[lytA]]-[[lytB]]-[[lytC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation (Asp) by [[YvrG]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]

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

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

* '''Interactions:''' [[YvrG]]-[[YvrHb]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16306698 PubMed]

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

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94504 P94504]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33220]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10094672,18820022,,16306698, </pubmed>

[[Category:Protein-coding genes]]

CitG

2009-12-07T09:23:52Z

Jourde:

* '''Description:''' fumarase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || fumarate hydratase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|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''' || 50 kDa, 5.475
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1386 bp, 462 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuxN]], [[gerAA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15294]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33040

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10384]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate = fumarate + H2O (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1YFE 1YFE] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P07343 P07343]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33040]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.2 4.2.1.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citG]]''

* '''Sigma factor:''' [[SigA]], [[SigH]]

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP718 (spec), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1122 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)

* '''lacZ fusion:''' pGP387 (in [[pAC7]]), available in [[Stülke]] lab

* '''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>2509422,, </pubmed>

[[Category:Protein-coding genes]]

CcpA

2009-12-07T09:22:50Z

Jourde:

* '''Description:''' Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ccpA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''graR, alsA, amyR''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator ([[LacI family]])
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates carbon catabolite repression (CCR)
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/nucleosides_catabolism.html Nucleoside catabolism], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val], [http://subtiwiki.uni-goettingen.de/pathways/histidine.html His], [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36,8 kDa, 5.06
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1002 bp, 334 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[motP]]'', ''[[aroA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14952]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ccpA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29740

===Phenotypes of a mutant ===

Loss of carbon catabolite repression.
Loss of [[PTS]]-dependent sugar transport due to excessive phosphorylation of [[PtsH |HPr]] by [[HprK]].
The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10376]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' transcriptional regulator of carbon catabolite repression (CCR)

* '''Protein family:''' [[LacI family]]

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

=== Genes controlled by CcpA ===

* '''Activation by CcpA:''' ''[[pta]]'', ''[[ackA]]'', ''[[ilvB]]-[[ilvH]]-[[ilvC]]-[[leuA]]-[[leuB]]-[[leuC]]-[[leuD]]''

* '''Repression by CcpA:''' ''[[abbA]], [[amyE]]'', ''[[bglP]]-[[bglH]]'', ''[[bglS]]'', ''[[cccA]]'', ''[[citZ]]-[[icd]]-[[mdh]]'', ''[[levD]]-[[levE]]-[[levF]]-[[levG]]-[[sacC]]'', ''[[licB]]-[[licC]]-[[licA]]-[[licH]]'', ''[[phoP]]-[[phoR]]'', ''[[xylA]]-[[xylB]]'', ''[[xynP]]-[[xynB]]''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** HTH lacI-type Domain (1 – 58)
** DNA binding Domain (6 – 25)

* '''Modification:'''

* '''Cofactor(s):''' [[PtsH |HPr]]-Ser46-P, Crh-Ser-46-P

* '''Effectors of protein activity:'''glucose-6-phosphate, fructose-1,6-bisphosphate [http://www.ncbi.nlm.nih.gov/pubmed/17376479?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Pubmed]

* '''Interactions:''' CcpA-[[PtsH |HPr]] [http://www.ncbi.nlm.nih.gov/pubmed/15369672?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed], CcpA-[[Crh]] [http://www.ncbi.nlm.nih.gov/pubmed/16316990?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2JCG 2JCG] (Apoprotein from ''Bacillus megaterium''), CcpA-Crh-DNA-complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], complex with P-Ser-[[PtsH |HPr]] and sulphate ions [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39857 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P25144 P25144]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29740]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ccpA]] [[motP]] [[motS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]

* '''Additional information:''' there are about 3.000 molecules of CcpA per cell [http://www.ncbi.nlm.nih.gov/sites/entrez/8000527 PubMed]

=Biological materials =

* '''Mutant:''' QB5407 (spc), GP302 (erm), GP300 (an in frame deletion of ''[[ccpA]]''), available in [[Stülke]] lab

* '''Expression vector:''' pGP643 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:''' available in [[Hillen]] and [[Stülke]] labs

=Labs working on this gene/protein=

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

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

[[Milton H. Saier]], University of California at San Diego, USA [http://biology.ucsd.edu/faculty/saier.html Homepage]

[[Yasutaro Fujita]], University of Fukuyama, Japan

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

[[Oscar Kuipers]], University of Groningen, The Netherlands
[http://molgen.biol.rug.nl/molgen/index.php Homepage]

=Your additional remarks=

=References=

'''Reviews'''

<pubmed> 8598282 , 19202299,14665673,18628769 ,18359269, 18628769 </pubmed>

'''General and physiological studies'''

<pubmed>1904524 ,10941796 ,12123463,8000527, 18757537,16547058,14523131 </pubmed>

'''Global analyses (proteome, transcriptome)'''

<pubmed>12850135 ,11251851,10559165, 11160890,17183215 </pubmed>

'''Repression of target genes by CcpA'''

<pubmed>15150224 ,16166551 ,11929549 , 7913927 ,17827291 ,11985717 ,12100558,7592486 </pubmed>

'''Positive regulation of gene expression by CcpA'''

<pubmed>8226682 ,12193635 ,10559153 ,15916605, 9811655 ,10986270 </pubmed>

'''Control of CcpA activity'''

<pubmed>7623661 ,9973552 ,9334231 ,12051938, 9689125 </pubmed>

'''CcpA-DNA interaction'''

<pubmed>8596444 ,10666464 ,15885105,7665492 ,9254709 </pubmed>

'''Functional analysis of CcpA'''

<pubmed>10383986 ,10601226 ,11557150,9252590 ,9988473 </pubmed>

'''Structural analyses'''

<pubmed>15369672 ,16316990 ,17376479 </pubmed>

[[Category:Protein-coding genes]]

PfkA

2009-12-07T09:19:55Z

Jourde:

* '''Description:''' phosphofructokinase, glycolytic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pfkA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pfk''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 6-phosphofructokinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34,1 kDa, 6.14
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pyk]]'', ''[[accA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14879]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pfkA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29190

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12644]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation (Reversible) [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]

* '''Domains:'''
** 3 x nucleotide binding domain (ATP) (21–25), (154–158), (171–187)

* '''Modification:'''

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by citrate, PEP (Hill Coefficient 3) and Ca2+ (competes with Mg2+) in ''B. licheniformes'' [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed].
** Inhibited by ATP (competitively) and f6p (non-competitively) in ''G. stearothermophillus'' [http://www.ncbi.nlm.nih.gov/pubmed/8136379 PubMed]
** Activated by GDP and ADP in lower concentrations (1mM); above that inhibition, competing with the ATP for the binding site (in ''G. stearothermophillus'') [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]

* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MTO 1MTO] (mutant, complex with fructose-6-phosphate, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=4PFK 4PFK] (Geobacillus stearothermophilus), ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=58449 NCBI], Mutant form, complex with fructose-6-phosphate ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=21480 NCBI]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34529 O34529]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29190]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.11 2.7.1.11]

=== Additional information===
PfkA is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

=Expression and regulation=

* '''Operon:''' ''pfkA [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]

* '''Sigma factor:'''

* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP87, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP393, available in [[Stülke]] lab

* '''lacZ fusion:''' pGP511 (in [[pAC6]]), available in [[Stülke]] lab

* '''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=

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

=Your additional remarks=

=References=

<pubmed> 16479537,19193632, 11489127, 8136379, 7873536 4269800 </pubmed>

[[Category:Protein-coding genes]]

Pyk

2009-12-07T09:19:18Z

Jourde:

* '''Description:''' pyruvate kinase, glycolytic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pyk''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pykA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|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''' || 61,9 kDa, 4.88
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1755 bp, 585 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytzA]]'', ''[[pfkA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14878]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:pyk_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29180

===Phenotypes of a mutant ===

Unable to grow with non-PTS carbohydrates (such as glucitol or glycerol) as single carbon source.

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12661]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ADP + phosphoenolpyruvate --> ATP + pyruvate
** The reaction is irreversible under physiological conditions

* '''Protein family:''' PEP-utilizing enzyme family (according to Swiss-Prot) pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser36 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], phosphorylation on Ser536 or Ser546 [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], please note that the Seris not on position 536 but rather at 538

* '''Cofactor(s):''' Mg2+, K+

* '''Effectors of protein activity:'''
** Activated by PEP (Hill Coefficient 1,8) [http://www.ncbi.nlm.nih.gov/sites/entrez/4623707 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
** Allosterically activated by AMP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
** Activation by r5p and ADP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
** Inhibition by ADP and f16bp in high concentrations; and ATP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2E28 2E28] (Geobacillus stearothermophilus)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80885 P80885]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29180]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40 2.7.1.40]

=== Additional information===
The enzyme is a tetramer with four active sites [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[pfkA]] [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]

* '''Sigma factor:'''

* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP590 (cat), GP510 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Stülke]] lab
** expression in ''B. subtilis'', native protein: pGP1411 (in [[pBQ200]]), available in [[Stülke]] lab
** expression in ''B. subtilis'', N-terminal Strep-tag: pGP1409 (in [[pGP380]]), available in [[Stülke]] lab
** expression in ''B. subtilis'', C-terminal Strep-tag: pGP1410 (in [[pGP382]]), available in [[Stülke]] lab

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

* '''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=

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

=Your additional remarks=

=References=

<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 </pubmed>

[[Category:Protein-coding genes]]

CitZ

2009-12-07T09:18:37Z

Jourde:

* '''Description:''' citrate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|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''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[ytwI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:citZ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H2O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

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

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA, 2-oxoglutarate and NADH [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''

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

* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (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:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=

<pubmed>10348849,8045899,,10656796,12850135 17218307 12100558 9642180 8045898 8655569 4211224 4980242 </pubmed>

[[Category:Protein-coding genes]]

Mdh

2009-12-07T09:17:39Z

Jourde:

* '''Description:''' malate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD+ = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

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

* '''Regulation:''' ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
''[[mdh]]'': constitutive

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpC]]: transcription repression
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP385, 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:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 </pubmed>

[[Category:Protein-coding genes]]

GapB

2009-12-07T09:16:43Z

Jourde:

* '''Description:''' glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent, gluconeogenic enzyme 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde-3-phosphate dehydrogenase 2
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || anabolic enzyme in gluconeogenesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37,3 kDa, 6.47
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1020 bp, 340 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[speD]]'', ''[[ytcD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14862]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:gapB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29020

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12592]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H (according to Swiss-Prot)
** This reaction is part of the gluconeogenesis

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''
** Nucleotid bindinge domain (12-13)
** 2x Glyceraldehyde 3-phosphate binding domain (151-153) & (210-211)

* '''Modification:'''

* '''Cofactor(s):''' NADP (preferentially) and NAD [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34425 O34425]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29020]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.59 1.2.1.59]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[gapB]]-[[speD]]''

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]

* '''Regulation:''' repressed (70-times) by Glc, repressor [[CcpN]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]

* '''Regulatory mechanism:''' transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

=Your additional remarks=

=References=

<pubmed> 16479537,10799476,10844697 ,15720552,18586936,17114254</pubmed>

[[Category:Protein-coding genes]]

SdhC

2009-12-07T09:15:30Z

Jourde:

* '''Description:''' succinate dehydrogenase(cytochrome b558 subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (cytochrome b558 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|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, 9.831
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 606 bp, 202 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhA]], [[yslB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14805]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sdhC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28450

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10351]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' cytochrome b558 family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
* '''Cofactor(s):''' Fe

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''Interactions:''' [[SdhB]]-[[SdhC]] (as part of the [[SdhC]]-[[SdhB]]-[[SdhA]] complex)

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P08064 P08064]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28450]

* '''E.C. number:''' 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' SdhC is less expressed under conditions of extreme iron starvation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Regulatory mechanism:''' [[FsrA]]: translational repression, [[sRNA]] [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>6401289,1707123,2120540,7669765,18697947,1324713,3036777,2495271,2176107,3117551,10913269,18763711,12560550, 18697947 3910107 6799760 </pubmed>

[[Category:Protein-coding genes]]

SdhA

2009-12-07T09:14:47Z

Jourde:

* '''Description:''' succinate dehydrogenase (flavoprotein subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (flavoprotein subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|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''' || 65 kDa, 5.714
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1758 bp, 586 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhB]], [[sdhC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14804]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:sdhA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28440

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10352]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' FRD/SDH subfamily (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

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

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''Interactions:''' [[SdhA]]-[[SdhB]] (as part of the [[SdhC]]-[[SdhB]]-[[SdhA]] complex)

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P08065 P08065]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28440]

* '''E.C. number:''' 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>2987185,1707123,6401289,6406223,1324713,3036777,2495271,3027051,,17726680 18763711 17726680 16493705 3910107 6799760 12560550 </pubmed>

[[Category:Protein-coding genes]]

SdhB

2009-12-07T09:14:06Z

Jourde:

* '''Description:''' succinate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (iron-sulfur protein)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|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''' || 28 kDa, 7.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysmA]], [[sdhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14803]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:sdhB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28430

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10353]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' succinate dehydrogenase/fumarate reductase iron-sulfur protein family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''Interactions:''' [[SdhA]]-[[SdhB]], [[SdhB]]-[[SdhC]] (as part of the [[SdhC]]-[[SdhB]]-[[SdhA]] complex)

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P08066 P08066]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28430]

* '''E.C. number:'''EC 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>1707123,6401289,1324713,3036777,2495271,3027051,7748886,2837411,12560550, 3910107 6799760 </pubmed>

[[Category:Protein-coding genes]]

Obg

2009-12-07T09:12:34Z

Jourde:

* '''Description:''' GTP-binding protein involved in initiation of sporulation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''obg''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || GTP-binding protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || may be required to stimulate activity of the [[phosphorelay]] that activates [[Spo0A]]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.859
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1284 bp, 428 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||'' [[pheB]]'', ''[[spo0B]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14752]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:obg_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU27920

===Phenotypes of a mutant ===

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

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spo0B-obg.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10337]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Binds and hydrolyzes GTP and readily exchanges GDP for GTP

* '''Protein family:''' GTP1/OBG family (according to Swiss-Prot) Era/Obg family

* '''Paralogous protein(s):''' [[Era]], [[Obg]], [[YphC]], [[YsxC]], [[RbgA]], [[YqeH]], [[ThdF]], [[YyaF]], [[YnbA]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
Obg possesses 3 domains: A N-terminal glycine-rich domain (1–158), a GTP binding domain (159–342) and a C-terminal TGS domain (343–428). The TGS domain has no known function, but it is named for three protein families in which it is found, ThrRS, GTPase, and SpoT.

* '''Modification:'''

* '''Cofactor(s):'''
GDP, GTP and probably ppGpp

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

* '''Interactions:'''
Interaction with Rsb proteins.

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1LMZ 1LMZ], [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=1LNZ 1LNZ]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P20964 P20964]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27920]
* '''E.C. number:'''

=== Additional information===

The biochemical analysis of bacterial and human Obg proteins combined with the structural observation of the ppGpp nucleotide within the Obg active site suggest a potential role for ppGpp modulation of Obg function in ''B. subtilis''.

=Expression and regulation=

* '''Operon:''' ''[[spo0B]]-[[obg]]''

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP835, available in [[Stülke]] lab
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP843, available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

*[[Bill Haldenwang]], San Antonio, USA
*[[Naotake Ogasawara]], Nara, Japan

=Your additional remarks=

=References=

<pubmed>15325267,18689482,7961487,7961486,15583165,2537815,10781545,10419966,12427945,12429099 </pubmed>

[[Category:Protein-coding genes]]

HemA

2009-12-07T08:32:50Z

Jourde:

* '''Description:''' glutamyl-tRNA reductase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hemA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamyl-tRNA reductase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || porphyrin biosynthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.313
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1365 bp, 455 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hemX]]'', ''[[ysxD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14777]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:hemA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28170

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10340]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' L-glutamate 1-semialdehyde + NADP+ + tRNA(Glu) = L-glutamyl-tRNA(Glu) + NADPH (according to Swiss-Prot)

* '''Protein family:''' glutamyl-tRNA reductase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P16618 P16618]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28170]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.70 1.2.1.70]

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''
** repressed in the absence of hydrogen peroxide ([[PerR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed]

* '''Regulatory mechanism:'''
** [[PerR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10217486,8012594,7667267,1536660,1672867,8932315,11532148, </pubmed>

[[Category:Protein-coding genes]]

OdhB

2009-12-04T17:21:56Z

Jourde:

* '''Description:''' 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''odhB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citM ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase complex
(dihydrolipoamide transsuccinylase, E2 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|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''' || 45 kDa, 4.859
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1251 bp, 417 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yocS]], [[odhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13828]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:odhB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19360

===Phenotypes of a mutant ===

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

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10273]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine (according to Swiss-Prot)

* '''Protein family:''' sodium:bile acid symporter family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]]

* '''Localization:''' cell membrane (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P16263 P16263]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19360]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.1.61 2.3.1.61] 1

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[odhA]]''-''[[odhB]]'' {{PubMed|11976317}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1508153}}

* '''Regulation:'''
** repressed by glucose (2.4-fold) ([[CcpA]]) {{PubMed|12850135}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression {{PubMed|12850135}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''
** pGP1145 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (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:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>2500417,,1508153,12850135 18763711 12682299,11976317 </pubmed>

[[Category:Protein-coding genes]]

OdhA

2009-12-04T17:21:26Z

Jourde:

* '''Description:''' 2-oxoglutarate dehydrogenase (E1 subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''odhA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citK ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase (E1 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|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''' || 105 kDa, 5.871
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2823 bp, 941 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[odhB]], [[yojO]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13829]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:odhA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19370

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10272]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2 (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]]

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P23129 P23129]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19370]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.4.2 1.2.4.2]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[odhA]]''-''[[odhB]]'' {{PubMed|11976317}}

* '''Sigma factor:''' [[SigA]] {{PubMed|1508153}}

* '''Regulation:'''
** repressed by glucose (2.4-fold) ([[CcpA]]) {{PubMed|12850135}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression {{PubMed|12850135}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP671 (spc), GP665 (aphA3), GP684 (cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>2500417,,1508153, 11976317 12850135</pubmed>

[[Category:Protein-coding genes]]

GltA

2009-12-04T16:24:53Z

Jourde:

* '''Description:''' large subunit of glutamate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gltA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate synthase (large subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate biosynthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 168 kDa, 5.47
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 4560 bp, 1520 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltB]]'', ''[[gltC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13728]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:gltA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18450

===Phenotypes of a mutant ===

auxotrophic for glutamate

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10811]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2 L-glutamate + NADP+ = L-glutamine + 2-oxoglutarate + NADPH (according to Swiss-Prot) 2 L-glutamate + NADP(+) <=> L-glutamine + 2-oxoglutarate + NADPH

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** Glutamine amidotransferase type-2 domain (22-415)
** Nucleotide binding domain (1060-1112)

* '''Modification:'''

* '''Cofactor(s):''' 3Fe-4S, FAD, FMN

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

* '''Interactions:'''

* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18763711 PubMed], cytoplasm

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39812 P39812]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18450]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.13 1.4.1.13] 3 1.4.1.13]

=== Additional information===

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

=Expression and regulation=

* '''Operon:''' ''[[gltA]]-[[gltB]]'' {{PubMed|12823818}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2548995}}

* '''Regulation:'''
** expression activated by glucose (11 fold) ([[CcpA]], [[GltC]]) {{PubMed|12850135,14523131}}
** repressed by arginine ([[GltC]], [[RocG]]) {{PubMed|15150225}}
** expressed in the presence of ammonium {{PubMed|11029411}}
** repressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) {{PubMed|11029411}}

* '''Regulatory mechanism:'''
** [[GltC]]: transcription activation {{PubMed|2548995}}
** [[TnrA]]: transcription repression {{PubMed|11029411}}

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

=Biological materials =

* '''Mutant:''' GP807 (del ''gltAB''::''tet''), GP222 (''gltA'' under the control of p-xyl), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:''' pGP526 (in [[pAC7]]), pGP919 (in [[pAC5]]), available in [[Stülke]] lab

* '''GFP fusion:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=

<pubmed>12823818,,11029411,12850135 7559360 15150225 2548995 17183217, 17608797,17134717,14523131,12823818, 18326565,17981983,18763711 </pubmed>

[[Category:Protein-coding genes]]

GltB

2009-12-04T16:24:04Z

Jourde:

* '''Description:''' small subunit of glutamate synthase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gltB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate synthase (small subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate biosynthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54.6 kDa, 7.69
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1479 bp, 493 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yogA]]'', ''[[gltA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13727]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:gltB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18440

===Phenotypes of a mutant ===

auxotrophic for glutamate

=== Database entries ===

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

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12594]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2 L-glutamate + NADP+ = L-glutamine + 2-oxoglutarate + NADPH (according to Swiss-Prot) 2 L-glutamate + NADP(+) <=> L-glutamine + 2-oxoglutarate + NADPH

* '''Protein family:''' glutamate synthase family.

* '''Paralogous protein(s):''' none

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** nucleotide binding domain (NADP) (299–313)

* '''Modification:'''

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

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

* '''Interactions:'''

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34399 O34399]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18440]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.13 1.4.1.13] 3 1.4.1.13]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[gltA]]-[[gltB]]'' {{PubMed|12823818}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2548995}}

* '''Regulation:''' see ''[[gltA]]''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP807 (del ''gltAB''::''tet''), GP517 (ermC), both available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1119 (in [[pGP380]], for SPINE, expression in ''B. subtilis''), available in [[Stülke]] lab

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

* '''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=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

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

=Your additional remarks=

=References=

<pubmed>12823818,,11029411,7559360 15150225 2548995 17183217 17608797 17134717 14523131, 12823818 , 18326565 </pubmed>

[[Category:Protein-coding genes]]

NdoA

2009-12-04T14:35:36Z

Jourde:

* '''Description:''' [[RNase]] EndoA, MazF family toxin, cleaves cellular mRNAs at specific, but frequently occuring sites 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ndoA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydcE''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || endoribonuclease EndoA, MazF family toxin
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || plasmid partition
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 4.892
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 348 bp, 116 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ndoAI]]'', ''[[rsbR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12273]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ydcE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04660

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12092]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' pemK 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/explore.do?structureId=1NE8 1NE8]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96622 P96622]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04660]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ndoAI]]-[[ndoA]]'' {{PubMed|15882409}}

* '''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>15882409,, </pubmed>

[[Category:Protein-coding genes]]