SubtiWiki - User contributions [en]

PETM-11

2015-11-19T10:00:43Z

Aklewing:

[[File:pETM-11.png|250px|thumb|right|'''pWH844: click to enlarge''']]

* vector for the expression of proteins in ''E. coli'', the [[plasmid]] allows to fuse a His(6) tag to the N-terminus of the expressed protein that can be cleaved of by the TEV protease

* host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

* in ''E. coli'': ampicillin resistance

*constructed by EMBL

*sequencing primer:
*'''CZ103''': 5’-GAGGATCGAGATCTCGATC-3‘
*'''CZ104''': 5’-CTAGTTATTGCTCAGCGGTG-3‘

<pubmed> 16351710 </pubmed>

== Return to [[Plasmids]] ==

PETM-11

2015-11-19T10:00:23Z

Aklewing:

PETM-11

2015-11-19T09:59:37Z

Aklewing:

PETM-11

2015-11-19T09:58:04Z

Aklewing:

PETM-11

2015-11-19T09:57:20Z

Aklewing:

[[File:pETM-11.png|250px|thumb|right|'''pWH844: click to enlarge''']]

* vector for the expression of proteins in ''E. coli'', the [[plasmid]] allows to fuse a His(6) tag to the N-terminus of the expressed protein that can be cleaved of by the TEV protease

* host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

* in ''E. coli'': ampicillin resistance

*constructed by EMBL

*sequencing primer:
*'''CZ103''': 5’-GAGGATCGAGATCTCGATC-3‘
*'''CZ104''': 5’-CTAGTTATTGCTCAGCGGTG-3‘

<pubmed> 16351710 </pubmed>
== Return to [[Plasmids]] ==

PETM-11

2015-11-19T09:55:55Z

Aklewing:

[[File:pETM-11.png|250px|thumb|right|'''pWH844: click to enlarge''']]

* vector for the expression of proteins in ''E. coli'', the [[plasmid]] allows to fuse a His(6) tag to the N-terminus of the expressed protein that can be cleaved of by the TEV protease

* host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

* in ''E. coli'': ampicillin resistance

*from EMBL

*sequencing primer:
*'''CZ103''': 5’-GAGGATCGAGATCTCGATC-3‘
*'''CZ104''': 5’-CTAGTTATTGCTCAGCGGTG-3‘

<pubmed> 16351710 </pubmed>
== Return to [[Plasmids]] ==

PETM-11

2015-11-19T09:55:21Z

Aklewing:

[[File:pETM-11.png|250px|thumb|right|'''pWH844: click to enlarge''']]

* vector for the expression of proteins in ''E. coli'', the [[plasmid]] allows to fuse a His(6) tag to the N-terminus of the expressed protein that can be cleaved of by the TEV protease

* host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

* in ''E. coli'': ampicillin resistance

*from EMBL

*sequencing primer:
*'''CZ103''': 5’-GAGGATCGAGATCTCGATC-3‘
*'''CZ104''': 5’-CTAGTTATTGCTCAGCGGTG-3‘

<pubmed> 16351710 </pubmed>
== Return to [[Plasmids]] ==

PETM-11

2015-11-19T09:54:24Z

Aklewing:

[[File:pETM-11.png|250px|thumb|right|'''pWH844: click to enlarge''']]

* vector for the expression of proteins in ''E. coli'', the [[plasmid]] allows to fuse a His(6) tag to the N-terminus of the expressed protein that can be cleaved of by the TEV protease

* host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

* in ''E. coli'': ampicillin resistance

*from EMBL

*sequencing primer:
*'''CZ103''': 5’-GAGGATCGAGATCTCGATC-3‘
*'''CZ104''': 5’-CTAGTTATTGCTCAGCGGTG-3‘

<pubmed> 16351710 </pubmed>
== Return to [[Plasmids]] ==

PETM-11

2015-11-19T09:53:07Z

Aklewing: Created page with "'''pWH844: click to enlarge''' * vector for the expression of proteins in ''E. coli'', the plasmid allows to fuse a His(6) tag to t..."

[[File:pETM-11.png|250px|thumb|right|'''pWH844: click to enlarge''']]

* vector for the expression of proteins in ''E. coli'', the [[plasmid]] allows to fuse a His(6) tag to the N-terminus of the expressed protein that can be cleaved of by the TEV protease

* host: ''E. coli'' BL21(DE3)/pLysS, expression of the desired protein is induced by the addition of 1 mM IPTG to the culture

* in ''E. coli'': ampicillin resistance

*sequencing primer:
*'''CZ103''': 5’-GAGGATCGAGATCTCGATC-3‘
*'''CZ104''': 5’-CTAGTTATTGCTCAGCGGTG-3‘

<pubmed> 16351710 </pubmed>
== Return to [[Plasmids]] ==

File:PETM-11.png

2015-11-19T09:52:52Z

Aklewing:

CitB

2013-08-13T12:13:22Z

Aklewing: /* Biological materials */

* '''Description:''' [[trigger enzymes|trigger enzyme]]: aconitase and RNA binding protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[trigger enzymes|trigger enzyme]]: aconitate hydratase (aconitase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU18000 citB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitB CitB]
|-
|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''' || 99 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU18000 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU18000 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU18000 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:citB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU18000]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[trigger enzyme]]}},
{{SubtiWiki category|[[RNA binding regulators]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CcpA regulon]]}},
{{SubtiWiki regulon|[[CcpC regulon]]}},
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[FsrA regulon]]}}

=The [[CitB regulon]]: ''[[feuA]]-[[feuB]]-[[feuC]]-[[ybbA]]'', ''[[citZ]]''=

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18000

===Phenotypes of a mutant ===
* glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]

=== Additional information===
* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed|21821766}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** Citrate <=> isocitrate
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster {{PubMed|23354745,10468622}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' FeS cluster

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

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[CitG]]-[[CitB]] {{PubMed|20933603}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P09339 P09339]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18000]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.3 4.2.1.3]

=== Additional information===
* ''B. subtilis'' aconitase is both an enzyme and an RNA binding protein ([[moonlighting proteins|moonlighting protein]]) [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
* extensive information on the structure and enzymatic properties of CitB can be found at [http://www.proteopedia.org/wiki/index.php/Aconitase Proteopedia]

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citB_1926680_1929409_1 citB] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|1310745}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** repressed in the presence of glucose and glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** expressed upon transition into the stationary phase ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed], indirect negative regulation by [[AbrB]] {{PubMed|20817675}}
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repression by glucose + arginine ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed2]
** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
** [[FsrA]]: translational repression {{PubMed|18697947}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP683 (erm), available in [[Jörg Stülke]]'s lab
** GP1275 (erm), available in [[Jörg Stülke]]'s lab
** GP1441 (spc), available in [[Jörg Stülke]]'s lab
** 1A999 ( ''citB''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]

* '''Expression vector:
**GP1439 (''citB''-''Strep'' ''(spc)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Jörg Stülke]]'s lab
**pGP1810 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''
** pGP700 (in [[pAC5]]), available in [[Jörg Stülke]]'s lab

* '''GFP fusion:''' GP1434 (spc, based on [[pGP1870]]), available in [[Jörg Stülke]]'s lab

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

* '''Antibody:''' available in [[Linc Sonenshein]]'s lab

* '''FLAG-tag construct:'''
** GP1144 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
** GP1145 (kan), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=
* [[Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
* [[Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 12732309 2696478 18261896 18086213 </pubmed>
==Original publications==
<pubmed>18697947, 20097860,2118511,12591885,10656796,12591885,12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305,20933603 21099137 21446632 21821766 22389480 23139400 23354745 20817675</pubmed>
[[Category:Protein-coding genes]]

OdhA

2013-08-13T12:11:58Z

Aklewing: /* Biological materials */

* '''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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19370 odhA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/OdhA OdhA]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19370 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:odhA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=odhA_2108774_2111608_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:odhA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19370]]
|-
|}

__TOC__
 
 
 
 

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

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

=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:'''
** phosphorylated on Arg-66 and Arg-621 {{PubMed|22517742}}

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

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

* '''[[SubtInteract|Interactions]]:'''
** [[OdhA]]-[[OdhB]]-[[PdhD]] {{PubMed|20933603}}

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2jgd 2JGD] (from ''Escherichia coli'', 38% identity, 55% similarity) {{PubMed|17367808}}

* '''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===
* extensive information on the structure and enzymatic properties of 2-oxoglutarate dehydrogenase can be found at [http://www.proteopedia.org/wiki/index.php/2-Oxoglutarate_Dehydrogenase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[odhA]]''-''[[odhB]]'' {{PubMed|11976317}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=odhA_2108774_2111608_-1 odhA] {{PubMed|22383849}}

* '''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), GP684 (cat), GP1274 (cat) available in [[Jörg Stülke]]'s lab
** GP1276 (''odhAB''::''cat''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 10672230</pubmed>
==Original publications==
<pubmed>2500417,20933603,1508153, 11976317 12850135 22517742 22900538 </pubmed>

[[Category:Protein-coding genes]]

PycA

2013-08-13T12:10:35Z

Aklewing: /* Biological materials */

* '''Description:''' pyruvate carboxylase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pycA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ylaP ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate carboxylase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || replenishment of the oxaloacetate pool
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14860 pycA]
|-
|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/biotin/index.html Biotin]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 127 kDa, 5.407
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3444 bp, 1148 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ftsW]]'', ''[[ctaA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14860 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14860 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14860 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:pycA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pycA_1554185_1557631_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pycA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14860]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14860

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12660]

=== 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):''' biotin

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3BG5 3BG5] (''S. aureus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q9KWU4 Q9KWU4]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14860]

* '''E.C. number:''' 6.4.1.1

=== Additional information===
PycA binds to StrepTactin, and may be co-purified when purifying Strep-tagged proteins by [[SPINE]].

PycA is 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:''' ''[[pycA]]'' {{PubMed|20081037}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pycA_1554185_1557631_1 pycA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|20081037}}

* '''Regulation:'''
** subject to positive stringent control upon lysine starvation {{PubMed|20081037}}

* '''Regulatory mechanism:'''
** stringent response: due to presence of adenines at +1 and +2 positions of the transcript {{PubMed|20081037}}

* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]

=Biological materials =

* '''Mutant:''' GP793 (cat), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1289 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>18613815 12769720 10229653 9597748 7780827 </pubmed>
==Original publications==
<pubmed>18763711, 20081037</pubmed>

[[Category:Protein-coding genes]]

PycA

2013-08-13T12:10:19Z

Aklewing: /* Biological materials */

* '''Description:''' pyruvate carboxylase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pycA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ylaP ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate carboxylase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || replenishment of the oxaloacetate pool
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14860 pycA]
|-
|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/biotin/index.html Biotin]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 127 kDa, 5.407
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3444 bp, 1148 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ftsW]]'', ''[[ctaA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14860 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14860 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14860 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:pycA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pycA_1554185_1557631_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:pycA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14860]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14860

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12660]

=== 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):''' biotin

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

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

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

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3BG5 3BG5] (''S. aureus'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q9KWU4 Q9KWU4]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14860]

* '''E.C. number:''' 6.4.1.1

=== Additional information===
PycA binds to StrepTactin, and may be co-purified when purifying Strep-tagged proteins by [[SPINE]].

PycA is 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:''' ''[[pycA]]'' {{PubMed|20081037}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pycA_1554185_1557631_1 pycA] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|20081037}}

* '''Regulation:'''
** subject to positive stringent control upon lysine starvation {{PubMed|20081037}}

* '''Regulatory mechanism:'''
** stringent response: due to presence of adenines at +1 and +2 positions of the transcript {{PubMed|20081037}}

* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]

=Biological materials =

* '''Mutant:'''** GP793 (cat), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1289 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>18613815 12769720 10229653 9597748 7780827 </pubmed>
==Original publications==
<pubmed>18763711, 20081037</pubmed>

[[Category:Protein-coding genes]]

SdhB

2013-08-13T12:09:16Z

Aklewing: /* Biological materials */

* '''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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28430 sdhB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SdhB SdhB]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28430 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28430 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28430 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sdhB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhB_2905571_2906332_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sdhB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28430]]
|-
|}

__TOC__
 
 
 
 

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

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

=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]

* '''[[SubtInteract|Interactions]]:'''
** [[SdhA]]-[[SdhB]], [[SdhB]]-[[SdhC]] (as part of the [[SdhC]]-[[SdhB]]-[[SdhA]] complex)
** part of a [[Respiratory complexes and supercomplexes|respiratory supercomplex]] {{PubMed|23880299}}

* '''[[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]
* extensive information on the structure and enzymatic properties of succinate dehydrogenase can be found at [http://www.proteopedia.org/wiki/index.php/Succinate_Dehydrogenase Proteopedia]

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhB_2905571_2906332_-1 sdhB] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[FsrA]]: translation inhibition {{PubMed|22389480}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** GP792 (''sdhCAB''::''phleo''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1436 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1426 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=
== Reviews ==
<pubmed> 11803018 </pubmed>
== Original publications ==
<pubmed>1707123,6401289,1324713,3036777,2495271,3027051,7748886,2837411,12560550, 3910107 6799760 22389480 23880299</pubmed>

[[Category:Protein-coding genes]]

SdhA

2013-08-13T12:08:36Z

Aklewing: /* Biological materials */

* '''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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28440 sdhA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SdhA SdhA]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28440 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28440 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28440 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:sdhA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhA_2906335_2908095_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sdhA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28440]]
|-
|}

__TOC__
 
 
 
 

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

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

=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]

* '''[[SubtInteract|Interactions]]:'''
** [[SdhA]]-[[SdhB]] (as part of the [[SdhC]]-[[SdhB]]-[[SdhA]] complex)
** [[FloT]]-[[SdhA]] {{PubMed|23651456}}
** part of a [[Respiratory complexes and supercomplexes|respiratory supercomplex]] {{PubMed|23880299}}

* '''[[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 membrane-bound trimer [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
** One subunit is bound to cytochrome 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]
* extensive information on the structure and enzymatic properties of succinate dehydrogenase can be found at [http://www.proteopedia.org/wiki/index.php/Succinate_Dehydrogenase Proteopedia]

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhA_2906335_2908095_-1 sdhA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:'''
** constitutive
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[FsrA]]: translation inhibition {{PubMed|22389480}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab
** GP792 (''sdhCAB''::''phleo''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
== Reviews ==
<pubmed> 11803018 </pubmed>
== Original publications ==
<pubmed>2987185,1707123,6401289,6406223,1324713,3036777,2495271,3027051,22389480,17726680 18763711 17726680 16493705 3910107 6799760 12560550 23651456 23880299</pubmed>
[[Category:Protein-coding genes]]

SdhC

2013-08-13T12:07:51Z

Aklewing: /* Biological materials */

* '''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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28450 sdhC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SdhC SdhC]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28450 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28450 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28450 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sdhC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhC_2908129_2908737_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sdhC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28450]]
|-
|}

__TOC__
 
 
 
 

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

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

=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]

* '''[[SubtInteract|Interactions]]:'''
** [[SdhB]]-[[SdhC]] (as part of the [[SdhC]]-[[SdhB]]-[[SdhA]] complex)
** part of a [[Respiratory complexes and supercomplexes|respiratory supercomplex]] {{PubMed|23880299}}

* '''[[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]
* extensive information on the structure and enzymatic properties of succinate dehydrogenase can be found at [http://www.proteopedia.org/wiki/index.php/Succinate_Dehydrogenase Proteopedia]

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sdhC_2908129_2908737_-1 sdhC] {{PubMed|22383849}}

* '''[[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]
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}

* '''Regulatory mechanism:'''
** [[FsrA]]: translation inhibition {{PubMed|22389480}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab
** GP792 (''sdhCAB''::''phleo''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
== Reviews ==
<pubmed> 11803018 </pubmed>
== Original publications ==
<pubmed>6401289,1707123,2120540,7669765,18697947,1324713,3036777,2495271,2176107,3117551,10913269,18763711,12560550, 18697947 3910107 6799760 21641999 22389480 23880299</pubmed>

[[Category:Protein-coding genes]]

Mdh

2013-08-13T12:06:56Z

Aklewing: /* Biological materials */

* '''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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29120 mdh]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Mdh Mdh]
|-
|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''' || 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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29120 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:mdh_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mdh_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29120]]
|-
|}

__TOC__
 
 
 
 

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

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

=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:'''
** phosphorylated on Arg-156 {{PubMed|22517742}}
** phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''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]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}

* '''[[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]
* extensive information on the structure and enzymatic properties of Mdh can be found at [http://www.proteopedia.org/wiki/index.php/Malate_dehydrogenase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 mdh] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** ''[[mdh]]'': constitutive

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719(spc) & GP1150(spc), available in [[Stülke]] lab
** GP790 (''citZ,icd,mdh''::''kan''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP385: for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)
** GP1438(''mdh''-''Strep'' ''(spc)'') & GP1440(''mdh''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1431 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

* '''YFP fusion:''' GP1429 (spc, based on [[pGP1871]]), available in the [[Stülke]] lab

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

* '''Antibody:'''

* '''FLAG-tag construct:'''
** GP1130 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603 22517742 23136871</pubmed>

[[Category:Protein-coding genes]]

Icd

2013-08-13T12:06:30Z

Aklewing: /* Biological materials */

* '''Description:''' isocitrate dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''icd''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29130 icd]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Icd Icd]
|-
|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 kDa, 4.833
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mdh]], [[citZ]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29130 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29130 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29130 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:icd_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=icd_2979716_2980987_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:icd_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29130]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29130

===Phenotypes of a mutant ===
** reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]
** growth and sporulation defects of the mutant could be partially bypassed by deletion of the major citrate synthase gene (''[[citZ]]'') {{PubMed|10348849}}
=== 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+BG10856]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH (according to Swiss-Prot)

* '''Protein family:''' isocitrate and isopropylmalate dehydrogenases 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/4147570 PubMed]

* '''Domains:'''

* '''Modification:'''
** phosphorylated on Arg-180 {{PubMed|22517742}}
** phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
** ''in vitro'' phosphorylated by [[PrkC]] on Thr-138, Thr-147, and Thr-396 {{PubMed|20389117}}

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

* '''Effectors of protein activity:'''
** Inhibited by glyoxylate, oxaloacetate and oxalomalate [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
*** Better inhibition when glyoxylate and oxaloacetate is combined, probably due to the non-enzymatic conversion into oxalomalate, which is a strong inhibitor [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''[[SubtInteract|Interactions]]:'''
** homodimer [http://www.ncbi.nlm.nih.gov/pubmed/11290745 PubMed]
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
** [[GltA]]-[[Icd]] {{PubMed|20933603}}
** [[OdhB]]-[[Icd]] {{PubMed|20933603}}

* '''[[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=1HQS 1HQS]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39126 P39126]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29130]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.42 1.1.1.42]

=== Additional information===
* This enzyme requires NADP+ exclusively. No activity was seen on the presence on NAD+ [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
* extensive information on the structure and enzymatic properties of Icd can be found at [http://www.proteopedia.org/wiki/index.php/Isocitrate_dehydrogenase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
**''[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=icd_2979716_2980987_-1 icd] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}

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

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Jörg Stülke]]'s lab
** 1A1000 ( ''icd''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1000&Search=1A1000 BGSC]
** 1A999 ( ''icd''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]
** GP790 (''citZ,icd,mdh''::''kan''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1121 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:''' available in [[Linc Sonenshein]]'s 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]

=Your additional remarks=

=References=

<pubmed>10656796,12850135 11290745 10348849 11751849 18763711 17726680 16493705 4147570 20389117 9244258 20933603 22517742</pubmed>

[[Category:Protein-coding genes]]

SucD

2013-08-13T12:05:21Z

Aklewing: /* Biological materials */

* '''Description:''' succinyl-CoA synthetase (alpha subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (alpha subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16100 sucD]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SucD SucD]
|-
|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''' || 31 kDa, 5.587
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sucC]], [[dprA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16100 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sucD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucD_1681617_1682519_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sucD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16100]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16100

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12681]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' succinate/malate CoA ligase alpha subunit family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [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]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Ser-19 OR Thr-20) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [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]
** GTP is not accepted by the enzyme [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]

* '''[[SubtInteract|Interactions]]:'''
** [[SucC]]-[[SucD]] {{PubMed|20933603}}

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

=== Database entries ===

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

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80865 P80865]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16100]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
* extensive information on the structure and enzymatic properties of succinyl-CoA synthetase can be found at [http://www.proteopedia.org/wiki/index.php/Succinyl-Coa_Synthetase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[sucD]]'' {{PubMed|11976317}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucD_1681617_1682519_1 sucD] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) {{PubMed|12850135}}

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression {{PubMed|12850135}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP720 (spc), available in [[Stülke]] lab
** 1A1008 ( ''sucD''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1008&Search=1A1008 BGSC]
** GP791 (''sucCD''::''tet''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:''' GP1435 (spc, based on [[pGP1870]]), available in the [[Stülke]] lab

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

* '''Antibody:'''

* '''FLAG-tag construct:''' GP1425 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307 11976317 20933603</pubmed>

[[Category:Protein-coding genes]]

CitZ

2013-08-13T12:03:59Z

Aklewing: /* Biological materials */

* '''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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29140 citZ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitZ CitZ]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29140 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29140 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29140 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:citZ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citZ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29140]]
|-
|}

__TOC__
 
 
 
 

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

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

=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]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}

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

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
** [http://www.rcsb.org/pdb/101/motm.do?momID=93 A discussion of citrate synthase structure]
* '''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===
* extensive information on the structure and enzymatic properties of CitZ can be found at [http://www.proteopedia.org/wiki/index.php/Citrate_synthase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 citZ] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** repression by glucose (6.7-fold) ([[CcpA]]) {{PubMed|12100558,12850135}}
** repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** reduced expression at excess citrate concentrations or iron depletion ([[CitB]]) {{PubMed|23354745}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** [[CitB]]: mRNA destabilization upon citrate accumulation or iron limitation {{PubMed|23354745}}

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

=Biological materials =

* '''Mutant:''' GP678 (erm), GP797 (spec) available in [[Jörg Stülke]]'s lab
** 1A999 ( ''citZ''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]
** GP790 (''citZ,icd,mdh''::''kan''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP1776 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)
** pGP1761 (expression with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[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=
==Reviews==
<pubmed>3013232 </pubmed>
==Original publications==
Additional publications: {{PubMed|22900538}}
<pubmed>10348849,8045899,,10656796,12850135 17218307 12100558 9642180 8045898 8655569 4211224 4980242 20525796 20933603 23354745 </pubmed>

[[Category:Protein-coding genes]]

CitZ

2013-08-13T12:03:36Z

Aklewing: /* Biological materials */

* '''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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29140 citZ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitZ CitZ]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29140 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29140 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29140 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:citZ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citZ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29140]]
|-
|}

__TOC__
 
 
 
 

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

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

=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]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}

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

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
** [http://www.rcsb.org/pdb/101/motm.do?momID=93 A discussion of citrate synthase structure]
* '''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===
* extensive information on the structure and enzymatic properties of CitZ can be found at [http://www.proteopedia.org/wiki/index.php/Citrate_synthase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 citZ] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** repression by glucose (6.7-fold) ([[CcpA]]) {{PubMed|12100558,12850135}}
** repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** reduced expression at excess citrate concentrations or iron depletion ([[CitB]]) {{PubMed|23354745}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** [[CitB]]: mRNA destabilization upon citrate accumulation or iron limitation {{PubMed|23354745}}

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

=Biological materials =

* '''Mutant:''' GP678 (erm), GP797 (spec) available in [[Jörg Stülke]]'s lab
** 1A999 ( ''citZ''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]
** GP790 (''citz, icd, mdh''::''kan''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP1776 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)
** pGP1761 (expression with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[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=
==Reviews==
<pubmed>3013232 </pubmed>
==Original publications==
Additional publications: {{PubMed|22900538}}
<pubmed>10348849,8045899,,10656796,12850135 17218307 12100558 9642180 8045898 8655569 4211224 4980242 20525796 20933603 23354745 </pubmed>

[[Category:Protein-coding genes]]

SucC

2013-08-13T12:01:34Z

Aklewing: /* Biological materials */

* '''Description:''' succinyl-CoA synthetase (beta subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (beta subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16090 sucC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SucC SucC]
|-
|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, 4.846
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqH]], [[sucD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16090 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sucC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucC_1680431_1681588_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sucC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16090]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16090

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12680]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [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]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-220 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [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]
*** GTP is not accept by the enzyme [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]

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}
** [[SucC]]-[[SucD]] {{PubMed|20933603}}

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

=== Database entries ===

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

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80886 P80886]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16090]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
* extensive information on the structure and enzymatic properties of succinyl-CoA synthetase can be found at [http://www.proteopedia.org/wiki/index.php/Succinyl-Coa_Synthetase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[sucD]]'' {{PubMed|11976317}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucC_1680431_1681588_1 sucC] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.7-fold) ([[CcpA]]) {{PubMed|12850135}}

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression {{PubMed|12850135}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1A1006 ( ''sucC''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1006&Search=1A1006 BGSC]
** GP1134 (cat), available in [[Jörg Stülke]]'s lab
** GP791 (''sucCD''::''tet''), available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22900538}}
<pubmed>12850135 17218307 11976317 20933603 </pubmed>

[[Category:Protein-coding genes]]

SucC

2013-08-13T12:01:13Z

Aklewing: /* Biological materials */

* '''Description:''' succinyl-CoA synthetase (beta subunit) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (beta subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16090 sucC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SucC SucC]
|-
|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, 4.846
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqH]], [[sucD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16090 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sucC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucC_1680431_1681588_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sucC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16090]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16090

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12680]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [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]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-220 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

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

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [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]
*** GTP is not accept by the enzyme [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]

* '''[[SubtInteract|Interactions]]:'''
** [[Mdh]]-[[SucC]] {{PubMed|20933603}}
** [[SucC]]-[[SucD]] {{PubMed|20933603}}

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

=== Database entries ===

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

* '''UniProt:''' [http://www.uniprot.org/uniprot/P80886 P80886]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16090]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
* extensive information on the structure and enzymatic properties of succinyl-CoA synthetase can be found at [http://www.proteopedia.org/wiki/index.php/Succinyl-Coa_Synthetase Proteopedia]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[sucD]]'' {{PubMed|11976317}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sucC_1680431_1681588_1 sucC] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.7-fold) ([[CcpA]]) {{PubMed|12850135}}

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression {{PubMed|12850135}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1A1006 ( ''sucC''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1006&Search=1A1006 BGSC]
** GP1134 (cat), available in [[Jörg Stülke]]'s lab
** GP791 (''sucCD''::''tet'')available in [[Jörg Stülke]]'s lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22900538}}
<pubmed>12850135 17218307 11976317 20933603 </pubmed>

[[Category:Protein-coding genes]]

YdaK

2013-08-13T11:40:45Z

Aklewing: /* Biological materials */

* '''Description:''' general stress protein, may act as c-di-GMP receptor 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ydaK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || general stress protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU04280 ydaK]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 6.695
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 849 bp, 283 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydaJ]]'', ''[[ydaL]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU04280 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU04280 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU04280 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ydaK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaK_480013_480864_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ydaK_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU04280]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU04280

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12058]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** contains a C-terminal degenerated GGDEF domain {{PubMed|23893111}}

* '''Modification:'''

* '''Cofactor(s):'''
** binds c-di-GPM at high concentration (K(D) for c-di-GMP: 1.1 myM) {{PubMed|23893111}}

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96585 P96585]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04280]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[ydaJ]]-[[ydaK]]-[[ydaL]]-[[ydaM]]-[[ydaN]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaK_480013_480864_1 ydaK] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigB]] {{PubMed|22383849}}

* '''Regulation:'''
** expressed during stress ([[SigB]]) {{PubMed|22383849}}

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1592 (kan) available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>22383849 22821967 23893111 </pubmed>

[[Category:Protein-coding genes]]

DgcP

2013-08-13T11:40:03Z

Aklewing: /* Biological materials */

* '''Description:''' diguanylate cyclase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''dgcP''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ytrP''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || diguanylate cyclase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of c-di-GMP
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29650 dgcP]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 5.695
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1737 bp, 579 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytsP]]'', ''[[rpsD]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29650 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29650 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29650 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:ytrP_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytrP_3033696_3035435_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ytrP_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29650]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29650

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13918]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** synthesis of c-di-GMP from two molecules of GTP {{PubMed|23893111}}

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** contains an N-terminal GAF domain {{PubMed|23893111}}
** contains a C-terminal GGDEF domain {{PubMed|22821967}}

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34325 O34325]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29650]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytrP_3033696_3035435_-1 dgcP] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1591 (tet) available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 23893111 22821967</pubmed>

[[Category:Protein-coding genes]]

PdeH

2013-08-13T11:36:52Z

Aklewing: /* Biological materials */

* '''Description:''' c-di-GMP degrading phosphodiesterase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pdeH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yuxH, comB, yufA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || c-di-GMP degrading phosphodiesterase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || degradation of c-di-GMP
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU31740 pdeH]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 5.36
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1227 bp, 409 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuzC]]'', ''[[pncB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU31740 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU31740 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU31740 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yuxH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yuxH_3258037_3259266_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yuxH_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU31740]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31740

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10377]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** degradation of c-di-GMP {{PubMed|23893111}}

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** contains an EAL domain {{PubMed|22821967}}

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P14203 P14203]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31740]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.71 3.1.3.71]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[pdeH]]'' {{PubMed|2507523}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yuxH_3258037_3259266_-1 pdeH] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2507523}}

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed|14651647,15687200}}

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression {{PubMed|14651647,15687200}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP1590 (kan) available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>14651647,15687200,2507523 22821967 23893111 </pubmed>

[[Category:Protein-coding genes]]

CitZ

2013-08-13T11:35:47Z

Aklewing: /* Biological materials */

* '''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"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29140 citZ]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/CitZ CitZ]
|-
|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]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29140 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29140 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29140 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:citZ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:citZ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29140]]
|-
|}

__TOC__
 
 
 
 

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

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

=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]

* '''[[SubtInteract|Interactions]]:'''
** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}

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

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]
** [http://www.rcsb.org/pdb/101/motm.do?momID=93 A discussion of citrate synthase structure]
* '''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===
* extensive information on the structure and enzymatic properties of CitZ can be found at [http://www.proteopedia.org/wiki/index.php/Citrate_synthase Proteopedia]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=citZ_2981151_2982269_-1 citZ] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8045899}}

* '''Regulation:'''
** repression by glucose (6.7-fold) ([[CcpA]]) {{PubMed|12100558,12850135}}
** repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
** reduced expression at excess citrate concentrations or iron depletion ([[CitB]]) {{PubMed|23354745}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
** [[CitB]]: mRNA destabilization upon citrate accumulation or iron limitation {{PubMed|23354745}}

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

=Biological materials =

* '''Mutant:''' GP678 (erm), GP797 (spec) available in [[Stülke]] lab
** 1A999 ( ''citZ''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP1776 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Stülke]] lab)
** pGP1761 (expression with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[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=
==Reviews==
<pubmed>3013232 </pubmed>
==Original publications==
Additional publications: {{PubMed|22900538}}
<pubmed>10348849,8045899,,10656796,12850135 17218307 12100558 9642180 8045898 8655569 4211224 4980242 20525796 20933603 23354745 </pubmed>

[[Category:Protein-coding genes]]

YotH

2013-05-08T13:50:01Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to propionyl-CoA carboxylase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yotH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU19880 yotH]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.386
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 171 bp, 57 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yotI]]'', ''[[yotG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13879]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yotH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yotH_2154077_2154250_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yotH_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[SP-beta prophage]]}},
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19880

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13741]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31867 O31867]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19880]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yotH_2154077_2154250_-1 yotH] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>,9387222, </pubmed>

[[Category:Protein-coding genes]]

YlaK

2013-05-08T13:44:58Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to phosphate starvation inducible protein [[PhoH]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ylaK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU14810 ylaK]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 5.422
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1326 bp, 442 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylaJ]]'', ''[[ylaL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13354]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ylaK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ylaK_1549465_1550793_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ylaK_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14810

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13348]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07635 O07635]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14810]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ylaK_1549465_1550793_1 ylaK] {{PubMed|22383849}}

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

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

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12762842,12107147, </pubmed>

[[Category:Protein-coding genes]]

YlxY

2013-05-08T13:44:23Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to deacetylase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ylxY''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymxI ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16700 ylxY]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 9.364
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pnpA]]'', ''[[mlpA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13543]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ylxY_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ylxY_1741618_1742577_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ylxY_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16700

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11492]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P50850 P50850]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16700]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ylxY_1741618_1742577_1 ylxY] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>23123912</pubmed>
[[Category:Protein-coding genes]]

YmfH

2013-05-08T13:43:56Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to peptidase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ymfH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16860 ymfH]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.944
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1245 bp, 415 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ymfF]]'', ''[[ymfI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13559]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ymfH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymfH_1758314_1759600_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ymfH_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16860

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13428]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31766 O31766]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16860]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[ymfD]]-[[ymfF]]-[[ymfH]]'' {{PubMed|18502870}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymfH_1758314_1759600_1 ymfH] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[Mta]]: transcription activation {{PubMed|18502870}}

* '''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> 18502870</pubmed>
[[Category:Protein-coding genes]]

YmfI

2013-05-08T13:43:31Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to 3-oxoacyl- acyl-carrier protein reductase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ymfI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16870 ymfI]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.224
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 726 bp, 242 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ymfH]]'', ''[[ymfJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13560]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ymfI_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymfI_1759655_1760383_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ymfI_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16870

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13429]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31767 O31767]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16870]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ymfI_1759655_1760383_1 ymfI] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YycN

2013-05-08T13:41:32Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' putative acetyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yycN''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40290 yycN]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 18 kDa, 6.831
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 468 bp, 156 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yycO]]'', ''[[rapG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16066]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yycN_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yycN_4139679_4140149_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yycN_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU40290

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11467]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' acetyltransferase 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=1UFH 1UFH]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32293 O32293]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40290]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yycN_4139679_4140149_-1 yycN] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YxeK

2013-05-08T13:40:38Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to monooxygenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yxeK''
|-
|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''' || sulphur metabolism
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU39520 yxeK]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 5.668
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1323 bp, 441 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxeL]]'', ''[[yxeJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15988]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yxeK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yxeK_4060818_4062143_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yxeK_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU39520

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11887]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' ntaA/snaA/soxA(dszA) monooxygenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54950 P54950]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39520]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[yxeK]]-[[yxeL]]-[[yxeM]]-[[yxeN]]-[[yxeO]]-[[yxeP]]-[[yxeQ]]'' {{PubMed|10746760}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yxeK_4060818_4062143_-1 yxeK] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|16513748}}

* '''Regulation:'''
** repressed in the presence of cysteine ([[CymR]]) {{PubMed|16513748}}

* '''Regulatory mechanism:'''
** [[CymR]]: transcription repression {{PubMed|16513748}}

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J'' </big>
<big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>
<big>Mol Microbiol. 2011 81(6): 1459-1473. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21815947 PubMed:21815947]
<pubmed>10746760,,16513748, </pubmed>
[[Category:Protein-coding genes]]

YxeK

2013-05-08T13:40:23Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to monooxygenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yxeK''
|-
|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''' || sulphur metabolism
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU39520 yxeK]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 5.668
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1323 bp, 441 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxeL]]'', ''[[yxeJ]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15988]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yxeK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yxeK_4060818_4062143_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yxeK_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU39520

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11887]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' ntaA/snaA/soxA(dszA) monooxygenase family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54950 P54950]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39520]

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

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[yxeK]]-[[yxeL]]-[[yxeM]]-[[yxeN]]-[[yxeO]]-[[yxeP]]-[[yxeQ]]'' {{PubMed|10746760}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yxeK_4060818_4062143_-1 yxeK] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|16513748}}

* '''Regulation:'''
** repressed in the presence of cysteine ([[CymR]]) {{PubMed|16513748}}

* '''Regulatory mechanism:'''
** [[CymR]]: transcription repression {{PubMed|16513748}}

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

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J'' </big>
<big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>
<big>Mol Microbiol. 2011 81(6): 1459-1473. </big>
[http://www.ncbi.nlm.nih.gov/pubmed/21815947 PubMed:21815947]
<pubmed>10746760,,16513748, </pubmed>
[[Category:Protein-coding genes]]

YxbA

2013-05-08T13:38:48Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' putative D-aspartate ligase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yxbA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxaO, aslA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || putative D-aspartate ligase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU39900 yxbA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/aspartate_asparagine.html Asp, Asn]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 4.433
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 267 bp, 89 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxbB]]'', ''[[yxnB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB16026]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yxbA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=aslA_4098150_4098419_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yxbA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU39900

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxbBA-yxnB-asnH-yxaM.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11351]

=== 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/P46325 P46325]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39900]

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

=== Additional information===

=Expression and regulation=
* '''Operon:'''
** ''[[yxbB]]-[[yxbA]]-[[yxnB]]-[[asnH]]-[[yxaM]]'' {{PubMed|20185509,10746760}}
** ''[[yxbB]]-[[yxbA]]-[[yxnB]]'' {{PubMed|20185509}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=aslA_4098150_4098419_1 yxbA] {{PubMed|22383849}}

* '''Sigma factor:''' SigA {{PubMed|20185509}}

* '''Regulation:'''
** repressed by glucose (8-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15101989 PubMed]

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15101989 PubMed]

* '''Additional information:'''
** the tricistronic ''[[yxbB]]-[[yxbA]]-[[yxnB]]'' transcript is extremely stable, and stability is mediated by a 5'-proximal long sequence triplication preceding the ''[[yxbB]]'' open reading frame {{PubMed|20185509}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>10746760,12618455,10498721,20185509,12618455,15101989, </pubmed>

[[Category:Protein-coding genes]]

YvdA

2013-05-08T13:36:32Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to carbonic anhydrase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yvdA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU34670 yvdA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 6.878
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 591 bp, 197 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvdB]]'', ''[[yvcT]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15472]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yvdA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvdA_3561590_3562183_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yvdA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU34670

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12410]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O06983 O06983]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34670]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yvdA]]''-''[[yvdB]]'' {{PubMed|22383849}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvdA_3561590_3562183_-1 yvdA] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>22383849 </pubmed>
[[Category:Protein-coding genes]]

YvaM

2013-05-08T13:36:03Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to hydrolase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yvaM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU33640 yvaM]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 8.995
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 768 bp, 256 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[secG]]'', ''[[yvzC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15369]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yvaM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvaM_3455472_3456242_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yvaM_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33640

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14068]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' AB hydrolase superfamily (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/O32234 O32234]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33640]

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

=== Additional information===

=Expression and regulation=

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvaM_3455472_3456242_1 yvaM] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''
** repressed by [[RghR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16553878 PubMed]

* '''Regulatory mechanism:'''
** [[RghR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16553878 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>16553878, </pubmed>

[[Category:Protein-coding genes]]

YotE

2013-05-08T13:35:11Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to biotin carboxylase [[AccC]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yotE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU19910 yotE]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 10.053
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 144 bp, 48 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yotF]]'', ''[[yotD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13882]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yotE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yotE_2154705_2154851_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yotE_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[SP-beta prophage]]}},
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19910

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13738]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31870 O31870]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19910]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yotE_2154705_2154851_-1 yotE] {{PubMed|22383849}}

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

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>,9387222, </pubmed>

[[Category:Protein-coding genes]]

YvaK

2013-05-08T13:33:55Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' general stress protein, similar to carboxylesterase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yvaK''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU33620 yvaK]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.992
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 744 bp, 248 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rnr]]'', ''[[secG]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15367]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yvaK_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvaK_3454221_3454967_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yvaK_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
{{SubtiWiki category|[[sporulation proteins]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33620

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14066]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' A carboxylic ester + H2O = an alcohol + a carboxylate (according to Swiss-Prot)

* '''Protein family:''' lipase/esterase LIP3/bchO 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=1TQH 1TQH] (Geobacillus stearothermophilus)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32232 O32232]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33620]

* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.1.1 3.1.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[secG]]-[[yvaK]]-[[rnr]]-[[smpB]]-[[ssrA]]'' {{PubMed|17369301}}
** ''[[yvaK]]-[[rnr]]-[[smpB]]-[[ssrA]]'' {{PubMed|17369301}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvaK_3454221_3454967_-1 yvaK] {{PubMed|22383849}}

* '''Sigma factor:'''
** ''[[yvaK]]'': [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]

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

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>11544224, 17369301</pubmed>

[[Category:Protein-coding genes]]

YvaG

2013-05-08T13:33:25Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to 3-oxoacyl- acyl-carrier protein reductase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yvaG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU33590 yvaG]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.757
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvaF]]'', ''[[ssrA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15364]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yvaG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvaG_3449732_3450526_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yvaG_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33590

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14063]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== 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/explore.do?structureId=3T4X 3T4X] (from ''B. anthracis'', 80% identity, 96% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32229 O32229]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33590]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvaG_3449732_3450526_-1 yvaG] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YusZ

2013-05-08T13:32:54Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to retinol dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yusZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvxA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32980 yusZ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 9.17
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 840 bp, 280 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yusY/2]]'', ''[[mrgA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15287]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yusZ_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yusZ_3382633_3383475_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yusZ_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU32980

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10863]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' short-chain dehydrogenases/reductases (SDR) family (according to Swiss-Prot)

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

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

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

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37959 P37959]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32980]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yusZ_3382633_3383475_1 yusZ] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YugF

2013-05-08T13:32:09Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to dihydrolipoamide S-acetyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yugF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU31420 yugF]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 8.356
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 819 bp, 273 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[alaR]]'', ''[[yugE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15131]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yugF_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yugF_3227581_3228402_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yugF_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31420

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12360]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' dmpD/todF/xylF esterase 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/O05235 O05235]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31420]

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

=== Additional information===

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

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yugF_3227581_3228402_1 yugF] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>9274030 </pubmed>
[[Category:Protein-coding genes]]

YubC

2013-05-08T13:31:42Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to cysteine dioxygenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yubC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU31140 yubC]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 5.055
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 483 bp, 161 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yubD]]'', ''[[trnSL-Ala1]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15092]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yubC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cdoA_3193863_3194348_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yubC_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31140

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13952]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' L-cysteine + O2 = 3-sulfinoalanine (according to Swiss-Prot)

* '''Protein family:''' cysteine dioxygenase 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=3EQE 3EQE]

* '''UniProt:''' [http://www.uniprot.org/uniprot/O32085 O32085]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31140]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cdoA_3193863_3194348_1 yubC] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YtdA

2013-05-08T13:30:07Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to UTP-glucose-1-phosphate uridylyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ytdA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yzwA ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU30850 ytdA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 5.907
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 816 bp, 272 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yteA]]'', ''[[ytcA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15063]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ytdA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytdA_3154735_3155553_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ytdA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30850

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11199]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P42407 P42407]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30850]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytdA_3154735_3155553_-1 ytdA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YtcB

2013-05-08T13:29:41Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' putative UDP-glucose epimerase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ytcB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || putative UDP-glucose epimerase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU30870 ytcB]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 8.866
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 948 bp, 316 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytcA]]'', ''[[ytcC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15065]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ytcB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytcB_3157008_3157958_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ytcB_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30870

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13829]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34886 O34886]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30870]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytcB_3157008_3157958_1 ytcB] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YtcA

2013-05-08T13:28:36Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to to NDP-sugar dehydrogenase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ytcA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU30860 ytcA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 5.943
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1284 bp, 428 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytdA]]'', ''[[ytcB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15064]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ytcA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytcA_3155725_3157011_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ytcA_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU30860

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13828]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

* '''Paralogous protein(s):''' [[TuaD]], [[Ugd]]

=== 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/O34862 O34862]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU30860]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytcA_3155725_3157011_1 ytcA] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

[[Category:Protein-coding genes]]

YsnE

2013-05-08T13:28:07Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' similar to acetyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ysnE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU28330 ysnE]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.763
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 453 bp, 151 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysnD]]'', ''[[ysnF]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14793]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ysnE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ysnE_2898292_2898747_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ysnE_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28330

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12336]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:''' acetyltransferase 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=1YX0 1YX0]

* '''UniProt:''' [http://www.uniprot.org/uniprot/P94562 P94562]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28330]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''ysnE'' {{PubMed|8969504}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ysnE_2898292_2898747_1 ysnE] {{PubMed|22383849}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

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

YrrT

2013-05-08T13:27:42Z

Aklewing: /* Categories containing this gene/protein */

* '''Description:''' putative AdoMet-dependent methyltransferase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yrrT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || putative AdoMet-dependent methyltransferase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || methionine salvage
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU27280 yrrT]
|-
|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]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 4.974
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 639 bp, 213 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mtnN]]'', ''[[yrzA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14670]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yrrT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yrrT_2787846_2788487_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yrrT_expression.png|500px]]
|-
|}

__TOC__
 
 
 
 
 

 

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

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU27280

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yrrT-mtn-yrhABC.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13799]

=== 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/O32029 O32029]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27280]

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

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yrrT]]-[[mtnN]]-[[mccA]]-[[mccB]]-[[yrhC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17056751 PubMed]

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yrrT_2787846_2788487_-1 yrrT] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16513748 PubMed]

* '''Regulation:'''
** repressed in the presence of cysteine ([[CymR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16513748 PubMed]

* '''Regulatory mechanism:'''
** [[CymR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16513748 PubMed]
** [[Spx]]: transcription activation {{PubMed|12642660,16885442}}

* '''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>17056751,16513748, 12642660,16885442, </pubmed>

[[Category:Protein-coding genes]]