CitG - Revision history

Jstuelk: /* References */

2014-11-14T15:35:03Z

‎References

134.76.70.252 at 14:04, 17 April 2014

2014-04-17T14:04:29Z

134.76.70.252 at 09:49, 17 April 2014

2014-04-17T09:49:01Z

134.76.38.147 at 14:43, 2 April 2014

2014-04-02T14:43:00Z

Jstuelk at 16:40, 5 March 2014

2014-03-05T16:40:24Z

134.76.70.252 at 11:38, 7 January 2014

2014-01-07T11:38:22Z

134.76.70.252 at 09:20, 12 November 2013

2013-11-12T09:20:11Z

134.76.70.252 at 14:31, 16 May 2013

2013-05-16T14:31:53Z

134.76.70.252 at 11:14, 14 May 2013

2013-05-14T11:14:08Z

134.76.70.252 at 13:48, 13 May 2013

2013-05-13T13:48:57Z

← Older revision		Revision as of 15:35, 14 November 2014
Line 1:		Line 1:
−	* '''Description:~~''' fumarase<br/><br/>~~	+	{{#bank: CitG}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''citG''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| fumarate hydratase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| TCA cycle~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33040 citG]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CitG CitG]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=citG citG]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 50 kDa, 5.475~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1386 bp, 462 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yuxN]], [[yvzF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33040 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33040 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33040 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:citG_context.gif]]~~
−	~~<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fumC_3389024_3390412_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:citG_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33040]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[carbon core metabolism]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU33040
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU33040&redirect=T BSU33040]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citG.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10384]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' (S)-malate = fumarate + H<sub>2</sub>O (according to Swiss-Prot)
−
−	* '''Protein family:''' Fumarase subfamily (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[AnsB]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[Mdh]]-[[CitG]] {{PubMed\|20933603}}
−	** [[CitG]]-[[CitB]] {{PubMed\|20933603}}
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU33040&redirect=T BSU33040]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3R6Q 3R6Q] (aspartase from ''Bacillus'' sp. YM55-1, 43% identity, 77% similarity) {{PubMed\|21661762}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P07343 P07343]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33040]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.2 4.2.1.2]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[citG]]'' {{PubMed\|3923430}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fumC_3389024_3390412_-1 citG] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|3130545,2509422,2509423}}, [[SigH]] {{PubMed\|3130545,2509422}}
−
−	* '''Regulation:''' constitutive
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2427 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 9880 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 7597 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 4282 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 4666 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−	** GP718 (spec), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−	** pGP1122 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
−
−	* '''lacZ fusion:'''
−	** pGP387 (in [[pAC7]]), available in [[Jörg Stülke]]'s lab
−
−	* '''GFP fusion:''' GP1433 (spc, based on [[pGP1870]]), 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:'''
−	** GP1132 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>2509422,3923430 ,3130545 2509423 21661762 20933603 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 122: / Line 122: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 2427 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 9880 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''
 ** GP718 (spec), available in [[Jörg Stülke]]'s lab

@@ Line 120: / Line 120: @@
 * '''Additional information:'''
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citG.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3R6Q 3R6Q] (aspartase from ''Bacillus'' sp. YM55-1, 43% identity, 77% similarity) {{PubMed|21661762}}

@@ Line 42: / Line 42: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[carbon core metabolism]]}}
+{{SubtiWiki category|[[carbon core metabolism]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 62: / Line 63: @@
 === Additional information===
 =The protein=
@@ Line 80: / Line 78: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 112: / Line 110: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fumC_3389024_3390412_-1 citG] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|3130545,2509422,2509423}}, [[SigH]] {{PubMed|3130545,2509422}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|3130545,2509422,2509423}}, [[SigH]] {{PubMed|3130545,2509422}}
 * '''Regulation:''' constitutive
@@ Line 119: / Line 117: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 145: / Line 144: @@
 =References=
-'''Additional publications:''' {{PubMed|21661762}}
-<pubmed>2509422,3923430 ,3130545 2509423 20933603</pubmed>
+<pubmed>2509422,3923430 ,3130545 2509423 21661762 20933603 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 18: / Line 18: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CitG CitG]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=citG citG]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.475

@@ Line 16: / Line 16: @@
 |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=BSU33040 citG]
 |-
-|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/CitG CitG]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CitG CitG]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''

@@ Line 31: / Line 31: @@
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
-|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fumC_3389024_3390412_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:citG_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fumC_3389024_3390412_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:citG_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33040]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuxN]], [[yvzF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33040 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33040 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33040 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33040 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33040 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33040 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:citG_context.gif]]