SerA - Revision history

Jstuelk: /* Biological materials */

2014-05-21T11:02:10Z

‎Biological materials

134.76.70.252 at 14:14, 17 April 2014

2014-04-17T14:14:25Z

134.76.70.252 at 09:34, 17 April 2014

2014-04-17T09:34:42Z

134.76.38.147 at 14:05, 2 April 2014

2014-04-02T14:05:25Z

Jstuelk at 13:21, 5 March 2014

2014-03-05T13:21:54Z

134.76.70.252 at 11:06, 7 January 2014

2014-01-07T11:06:42Z

Jstuelk: /* References */

2013-06-04T11:18:32Z

‎References

134.76.70.252 at 13:47, 16 May 2013

2013-05-16T13:47:25Z

134.76.70.252 at 10:36, 14 May 2013

2013-05-14T10:36:06Z

134.76.70.252 at 13:10, 13 May 2013

2013-05-13T13:10:44Z

← Older revision		Revision as of 11:02, 21 May 2014
Line 1:		Line 1:
−	* '''Description:~~''' phosphoglycerate dehydrogenase <br/><br/>~~	+	{{#bank: SerA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''serA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| phosphoglycerate dehydrogenase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| biosynthesis of serine~~
−	\|-
−	\|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=BSU23070 serA]
−	\|-
−	\|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=serA serA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 56 kDa, 5.617~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1575 bp, 525 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ypzE]]'', ''[[aroC]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23070 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23070 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23070 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:serA_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=serA_2411086_2412663_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:serA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23070]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biosynthesis/ acquisition of amino acids]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU23070
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23070&redirect=T BSU23070]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10509]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' 3-phospho-D-glycerate + NAD<sup>+</sup> = 3-phosphonooxypyruvate + NADH (according to Swiss-Prot)
−
−	* '''Protein family:''' D-isomer specific 2-hydroxyacid dehydrogenase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−	** S-cysteinylation after diamide stress (C410)[http://www.ncbi.nlm.nih.gov/sites/entrez/17611193 PubMed]
−	** active site Cys410 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed\|21749987}} {{PubMed\|22938038}}
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23070&redirect=T BSU23070]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1YBA 1YBA] (from ''E. coli'', 30% identity, 52% similarity) {{PubMed\|15823035}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P35136 P35136]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23070]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.95 1.1.1.95]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''serA'' {{PubMed\|7934830}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serA_2411086_2412663_1 serA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** strongly repressed in response to glucose starvation in M9 medium {{PubMed\|23033921}}
−
−	* '''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): 6336 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 12316 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 9076 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 4149 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 5497 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−	** 1A614 ( ''serA''::''erm''), {{PubMed\|3015878}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A614&Search=1A614 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:''' pGP187 (in [[pAC7]]), available in [[Stülke]] lab
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>22938038,17611193,7934830 ,18763711,15823035 21749987 23033921 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 122: / Line 122: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 6336 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 12316 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''
 ** 1A614 ( ''serA''::''erm''), {{PubMed|3015878}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A614&Search=1A614 BGSC]

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

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serA.html]
@@ Line 92: / Line 93: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1YBA 1YBA] (from ''E. coli'', 30% identity, 52% similarity) {{PubMed|15823035}}

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},
-{{SubtiWiki category|[[membrane proteins]]}}
+{{SubtiWiki category|[[membrane proteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 61: / Line 62: @@
 === Additional information===
 =The protein=
@@ Line 79: / Line 77: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
@@ Line 85: / Line 83: @@
 ** active site Cys410 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed|21749987}} {{PubMed|22938038}}
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 111: / Line 109: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serA_2411086_2412663_1 serA] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 119: / Line 117: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 140: / Line 139: @@
 =References=
-<pubmed>22938038,17611193,7934830 ,18763711,15823035 21749987 23033921</pubmed>
+<pubmed>22938038,17611193,7934830 ,18763711,15823035 21749987 23033921 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=BSU23070 serA]
 |-
-|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/ala_gly_ser.html Ala, Gly, Ser]'''
+|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=serA serA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.617

@@ Line 29: / Line 29: @@
   <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=serA_2411086_2412663_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:serA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serA_2411086_2412663_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:serA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23070]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ypzE]]'', ''[[aroC]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23070 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23070 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23070 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23070 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23070 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23070 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:serA_context.gif]]