PdxS - Revision history

Jstuelk: /* References */

2015-02-16T16:39:00Z

‎References

Jstuelk at 09:26, 5 December 2014

2014-12-05T09:26:34Z

134.76.70.252 at 14:16, 17 April 2014

2014-04-17T14:16:34Z

134.76.70.252 at 09:41, 17 April 2014

2014-04-17T09:41:18Z

134.76.70.252 at 11:48, 8 April 2014

2014-04-08T11:48:38Z

134.76.38.147 at 12:44, 2 April 2014

2014-04-02T12:44:58Z

Jstuelk at 16:56, 5 March 2014

2014-03-05T16:56:45Z

134.76.70.252 at 14:12, 18 November 2013

2013-11-18T14:12:25Z

Jstuelk at 07:55, 9 July 2013

2013-07-09T07:55:02Z

Jstuelk at 07:53, 9 July 2013

2013-07-09T07:53:05Z

← Older revision		Revision as of 16:39, 16 February 2015
Line 1:		Line 1:
−	* '''Description:~~''' pyridoxal-5'-phosphate synthase (synthase domain) <br/><br/>~~	+	{{#bank: PdxS}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pdxS''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yaaD ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| pyridoxal-5'-phosphate synthase (synthase domain)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| pyridoxal-5'-phosphate biosynthesis~~
−	\|-
−	\|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=BSU00110 pdxS]
−	\|-
−	\|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=PdxS PdxS]
−	\|-
−	\|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=PdxS PdxS]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 31 kDa, 5.085~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 882 bp, 294 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[dacA]]'', ''[[pdxT]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00110 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yaaD_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=pdxS_19062_19946_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:pdxS_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00110]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biosynthesis of cofactors]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00110
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~auxotrophic for pyridoxal 5'-phosphate [http://www.ncbi.nlm.nih.gov/sites/entrez/14762015 PubMed]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00110&redirect=T BSU00110]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaDE.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10075]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' pdxS/SNZ family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−	** phosphorylated on Arg-8 {{PubMed\|22517742}}
−	** phosphorylated on STY [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[PdxS]]-[[PdxT]] {{PubMed\|25473090,14762015,16030023,17159152}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00110&redirect=T BSU00110]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore.do?structureId=2NV1 2NV1] [[PdxS]] {{PubMed\|17159152}}
−	** [http://www.rcsb.org/pdb/explore.do?structureId=2NV2 2NV2] [[PdxS]]-[[PdxT]] complex {{PubMed\|17159152}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37527 P37527]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00110]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[pdxS]]-[[pdxT]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdxS_19062_19946_1 pdxS] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:''' negatively controlled by [[Spo0A]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−	** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 6001 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 16290 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 7634 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 4624 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 7523 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>15911615,14762015,25473090,14651647, 17726680, 16493705, 16030023, 19152323,17159152 22517742 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 93: / Line 93: @@
 * '''[[SubtInteract|Interactions]]:'''
-**  [[PdxS]]-[[PdxT]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16030023 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/14762015 PubMed2]
+**  [[PdxS]]-[[PdxT]] {{PubMed|25473090,14762015,16030023,17159152}}
 * '''[[Localization]]:'''
@@ Line 153: / Line 153: @@
 =References=
-<pubmed>15911615,14762015,,14651647, 17726680, 16493705, 16030023, 19152323,17159152 22517742 15378759</pubmed>
+<pubmed>15911615,14762015,25473090,14651647, 17726680, 16493705, 16030023, 19152323,17159152 22517742 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 130: / Line 130: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 6001 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 16290 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 128: / Line 128: @@
 * '''Additional information:'''
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 17: / Line 17: @@
 |-
 |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=PdxS PdxS]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.085

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaDE.html]
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 41: / Line 41: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[biosynthesis of cofactors]]}},
-{{SubtiWiki category|[[phosphoproteins]]}}
+{{SubtiWiki category|[[phosphoproteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 63: / Line 64: @@
 === Additional information===
 =The protein=
@@ Line 81: / Line 79: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
@@ Line 87: / Line 85: @@
 ** phosphorylated on STY [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 125: / Line 123: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 146: / Line 145: @@
 =References=
-<pubmed>15911615,14762015,,14651647, 17726680, 16493705, 16030023, 19152323,17159152 22517742 </pubmed>
+<pubmed>15911615,14762015,,14651647, 17726680, 16493705, 16030023, 19152323,17159152 22517742 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=BSU00110 pdxS]
 |-
-|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/PdxS PdxS]
+|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=PdxS PdxS]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.085

@@ Line 99: / Line 99: @@
 * '''Structure:'''
-** [http://www.rcsb.org/pdb/explore.do?structureId=2NV1 2NV1] [[PdxS]]
+** [http://www.rcsb.org/pdb/explore.do?structureId=2NV1 2NV1] [[PdxS]] {{PubMed|17159152}}
-** [http://www.rcsb.org/pdb/explore.do?structureId=2NV2 2NV2] [[PdxS]]-[[PdxT]] complex
+** [http://www.rcsb.org/pdb/explore.do?structureId=2NV2 2NV2] [[PdxS]]-[[PdxT]] complex {{PubMed|17159152}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P37527 P37527]
@@ Line 116: / Line 116: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdxS_19062_19946_1 pdxS] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:''' negatively controlled by [[Spo0A]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
@@ Line 146: / Line 146: @@
 =References=
-<pubmed>15911615,14762015,,14651647, 17726680, 16493705, 14651647, 16030023, 14762015, 19152323,17159152 22517742 </pubmed>
+<pubmed>15911615,14762015,,14651647, 17726680, 16493705, 16030023, 19152323,17159152 22517742 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 102: / Line 98: @@
 === Database entries ===
-* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2NV2 2NV2]	[[PdxS]]-[[PdxT]] complex
+* '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P37527 P37527]
@@ Line 114: / Line 112: @@
 =Expression and regulation=
-* '''Operon:''' ''[[pdxS]]-[[pdxT]]''
+* '''Operon:''' ''[[pdxS]]-[[pdxT]]'' {{PubMed|22383849}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdxS_19062_19946_1 pdxS] {{PubMed|22383849}}