Tpi - Revision history

Jstuelk at 17:24, 16 May 2014

2014-05-16T17:24:04Z

134.76.70.252 at 14:15, 17 April 2014

2014-04-17T14:15:54Z

134.76.70.252 at 09:28, 17 April 2014

2014-04-17T09:28:14Z

134.76.38.147 at 14:47, 2 April 2014

2014-04-02T14:47:30Z

Jstuelk at 14:37, 5 March 2014

2014-03-05T14:37:09Z

134.76.70.252 at 11:41, 7 January 2014

2014-01-07T11:41:37Z

134.76.70.252 at 14:21, 18 November 2013

2013-11-18T14:21:21Z

Jstuelk at 15:36, 13 July 2013

2013-07-13T15:36:45Z

134.76.70.252 at 14:36, 16 May 2013

2013-05-16T14:36:03Z

134.76.70.252 at 11:17, 14 May 2013

2013-05-14T11:17:55Z

← Older revision		Revision as of 17:24, 16 May 2014
Line 1:		Line 1:
−	* '''Description:~~''' triose phosphate isomerase, glycolytic/ gluconeogenic enzyme<br/><br/>~~	+	{{#bank: Tpi}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''tpi''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''tpiA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| triosephosphate isomerase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| enzyme in glycolysis/ gluconeogenesis~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33920 tpi]
−	\|-
−	\|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=Tpi Tpi]
−	\|-
−	\|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=tpi tpi]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 26,9 kDa, 4.79~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 759 bp, 253 amino acids~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[pgm]]'', ''[[pgk]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33920 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33920 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33920 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:tpi_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=tpiA_3479405_3480166_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:tpi_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33920]]
−	\|-
−	\|}
−
−	~~__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]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CggR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU33920
−
−	~~===Phenotypes of a mutant ===~~
−	* essential {{PubMed\|12682299}}, non-essential according to {{PubMed\|23420519}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU33920&redirect=T BSU33920]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10897]
−
−	~~=== Additional information===~~
−	* 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:''' D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate (according to Swiss-Prot)
−
−	* '''Protein family:''' triosephosphate isomerase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' phosphorylation on Ser-213 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:''' inhibited by 2-phosphoglycolate (in ''B. stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/8580851 PubMed]
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[Tkt]]-[[Tpi]] {{PubMed\|19193632}}
−
−	* '''[[Localization]]:'''
−	** cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU33920&redirect=T BSU33920]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1BTM 1BTM] (complex with 2-phosphoglycolic acid, Geobacillus stearothermophilus), complex with 2-phosphpoglycolic acid, ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=48255 NCBI]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P27876 P27876]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33920]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.1 5.3.1.1]
−
−	~~=== Additional information===~~
−	* extensive information on the structure and enzymatic properties of Tpi can be found at [http://www.proteopedia.org/wiki/index.php/Triose_Phosphate_Isomerase Proteopedia]
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−	** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed\|11489127}}
−	** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed\|11489127}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tpiA_3479405_3480166_-1 tpi] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|11489127}}
−
−	* '''Regulation:'''
−	** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
−	** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed\|11489127}}
−	** ''[[pgk]]'': constitutive {{PubMed\|11489127}}
−
−	* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed\|11489127}}
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 4265 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 5061 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 2920 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 1493 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 2091 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:''' GP700 (cat), available in [[Jörg Stülke]]'s lab, {{PubMed\|23420519}}
−
−	* '''Expression vector:'''
−	** pGP394 (N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
−	** pGP89 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis), available in [[Jörg Stülke]]'s lab
−	** pGP1511 (expression in ''B. subtilis'', in [[pBQ200]]), 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:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>12850135 11489127 17505547 8021172 17218307 8580851 19193632 21821766 23420519 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 132: / Line 132: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 4265 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 5061 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:''' GP700 (cat), available in [[Jörg Stülke]]'s lab, {{PubMed|23420519}}

@@ Line 130: / Line 130: @@
 * '''Additional information:'''
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 60: / Line 60: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
@@ Line 97: / Line 98: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1BTM 1BTM] (complex with 2-phosphoglycolic acid, Geobacillus stearothermophilus),  complex with 2-phosphpoglycolic acid, ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=48255 NCBI]

@@ Line 44: / Line 44: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[carbon core metabolism]]}},
-{{SubtiWiki category|[[phosphoproteins]]}}
+{{SubtiWiki category|[[phosphoproteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 81: / Line 82: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:''' phosphorylation on Ser-213 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:''' inhibited by 2-phosphoglycolate (in ''B. stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/8580851 PubMed]
@@ Line 126: / Line 127: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 150: / Line 152: @@
 =References=
-<pubmed>12850135 11489127 17505547 8021172 17218307 8580851 19193632 21821766 23420519</pubmed>
+<pubmed>12850135 11489127 17505547 8021172 17218307 8580851 19193632 21821766 23420519 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=Tpi Tpi]
 |-
-|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], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
+|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=tpi tpi]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26,9 kDa, 4.79

@@ 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=BSU33920 tpi]
 |-
-|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/Tpi Tpi]
+|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=Tpi Tpi]
 |-
 |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], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''

@@ Line 129: / Line 129: @@
 =Biological materials =
-* '''Mutant:''' GP700 (cat), available in [[Stülke]] lab
+* '''Mutant:''' GP700 (cat), available in [[Jörg Stülke]]'s lab, {{PubMed|23420519}}
 * '''Expression vector:'''
-** pGP394 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
+** pGP394 (N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab
-** pGP89 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis), available in [[Stülke]] lab
+** pGP89 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis), available in [[Jörg Stülke]]'s lab
-** pGP1511 (expression in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
+** pGP1511 (expression in ''B. subtilis'', in [[pBQ200]]), available in [[Jörg Stülke]]'s lab
 * '''lacZ fusion:'''
@@ Line 140: / Line 140: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
 * '''Antibody:'''

@@ 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=tpiA_3479405_3480166_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:tpi_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tpiA_3479405_3480166_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:tpi_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU33920]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgm]]'', ''[[pgk]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33920 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33920 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33920 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU33920 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU33920 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU33920 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:tpi_context.gif]]