YwjH - Revision history

134.76.70.252 at 14:22, 17 April 2014

2014-04-17T14:22:49Z

134.76.70.252 at 09:41, 17 April 2014

2014-04-17T09:41:01Z

134.76.38.147 at 15:03, 2 April 2014

2014-04-02T15:03:33Z

Jstuelk at 16:01, 5 March 2014

2014-03-05T16:01:41Z

134.76.70.252 at 11:53, 7 January 2014

2014-01-07T11:53:21Z

134.76.70.252 at 14:49, 16 May 2013

2013-05-16T14:49:22Z

134.76.70.252 at 11:31, 14 May 2013

2013-05-14T11:31:15Z

134.76.70.252 at 14:05, 13 May 2013

2013-05-13T14:05:50Z

Fmeyer: /* Biological materials */

2012-11-02T08:08:11Z

‎Biological materials

134.76.70.252 at 16:57, 7 August 2012

2012-08-07T16:57:17Z

← Older revision		Revision as of 14:22, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' transaldolase <br/><br/>~~	+	{{#bank: YwjH}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ywjH''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| transaldolase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| pentose phosphate pathway~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU37110 ywjH]
−	\|-
−	\|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=ywjH ywjH]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 22 kDa, 5.876~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 636 bp, 212 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[murAB]]'', ''[[fbaA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37110 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ywjH_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=ywjH_3807754_3808392_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ywjH_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU37110]]
−	\|-
−	\|}
−
−	~~__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]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU37110
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37110&redirect=T BSU37110]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fbaA-ywjH.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10413]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate (according to Swiss-Prot)
−
−	* '''Protein family:''' Type 3B subfamily (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' phosphorylation on Ser-39 {{PubMed\|17218307,16493705,17726680}}, ''in vitro'' phosphorylated by [[PrkC]] {{PubMed\|20389117}}
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** forms decamers (dimer of pentamers) {{PubMed\|22212631}}
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37110&redirect=T BSU37110]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3R8R 3R8R] {{PubMed\|22212631}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P19669 P19669]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37110]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/2.2.1.2 2.2.1.2]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[fbaA]]-[[ywjH]]'' {{PubMed\|11489127}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywjH_3807754_3808392_-1 ywjH] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''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): 9591 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 25813 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−	** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP819, available in [[Stülke]] lab
−	** pGP1790 (expression of ''[[ywjH]]'' in ''B. subtilis'', in [[pGP1389]]), available in [[Stülke]] lab
−	** GP1409 (''ywjH''-''Strep'' ''(spc)'') & GP1411 (''ywjH''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
−
−	* '''Antibody:'''
−
−	* '''FLAG-tag construct:''' GP1407 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed> 17726680, 17218307, 16493705 11489127 20389117 21857661 22212631 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

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

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fbaA-ywjH.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3R8R 3R8R] {{PubMed|22212631}}

@@ Line 39: / Line 39: @@
 <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]]}}
+{{SubtiWiki category|[[phosphoproteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 67: / Line 64: @@
 === Additional information===
 =The protein=
@@ Line 85: / Line 79: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:''' phosphorylation on Ser-39 {{PubMed|17218307,16493705,17726680}}, ''in vitro'' phosphorylated by [[PrkC]] {{PubMed|20389117}}
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 116: / Line 110: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywjH_3807754_3808392_-1 ywjH] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 123: / Line 117: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 148: / Line 143: @@
 =References=
-'''Additional publications:''' {{PubMed|22212631}}
+<pubmed> 17726680, 17218307, 16493705 11489127 20389117 21857661 22212631 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=BSU37110 ywjH]
 |-
-|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=ywjH ywjH]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 5.876

@@ 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=ywjH_3807754_3808392_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ywjH_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywjH_3807754_3808392_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ywjH_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU37110]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[murAB]]'', ''[[fbaA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37110 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37110 DNA_with_flanks]
 |-
 |-

@@ Line 131: / Line 131: @@
 ** for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]]: pGP819, available in [[Stülke]] lab
 ** pGP1790 (expression of ''[[ywjH]]'' in ''B. subtilis'', in [[pGP1389]]), available in [[Stülke]] lab
-** GP1411 (''ywjH''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab
+** GP1409 (''ywjH''-''Strep'' ''(spc)'') & GP1411 (''ywjH''-''Strep'' ''(cat)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab
 * '''lacZ fusion:'''

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''