PdxT - Revision history

Jstuelk: /* References */

2015-02-16T16:39:19Z

‎References

Jstuelk at 09:27, 5 December 2014

2014-12-05T09:27:11Z

134.76.70.252 at 14:16, 17 April 2014

2014-04-17T14:16:36Z

134.76.70.252 at 09:38, 17 April 2014

2014-04-17T09:38:28Z

134.76.70.252 at 11:48, 8 April 2014

2014-04-08T11:48:35Z

134.76.38.147 at 12:45, 2 April 2014

2014-04-02T12:45:00Z

134.76.70.252 at 14:12, 18 November 2013

2013-11-18T14:12:27Z

Jstuelk: /* Database entries */

2013-07-09T07:55:20Z

‎Database entries

Jstuelk at 07:51, 9 July 2013

2013-07-09T07:51:17Z

134.76.70.252 at 12:16, 16 May 2013

2013-05-16T12:16:55Z

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

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pdxT''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yaaE ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| pyridoxal-5'-phosphate synthase (glutaminase 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=BSU00120 pdxT]
−	\|-
−	\|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=PdxT PdxT]
−	\|-
−	\|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=PdxT PdxT]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 21 kDa, 4.984~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 588 bp, 196 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[pdxS]]'', ''[[serS]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00120 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yaaE_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=pdxT_19968_20558_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:pdxT_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00120]]
−	\|-
−	\|}
−
−	~~__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]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00120
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00120&redirect=T BSU00120]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaDE.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10076]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' glutamine amidotransferase pdxT/SNO family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''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=BSU00120&redirect=T BSU00120]
−
−	* '''Structure:'''
−	** PdxT [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=43149 2NV0] {{PubMed\|17159152}}
−	** [[PdxS]]-[[PdxT]] complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=43151 2NV2] {{PubMed\|17159152}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37528 P37528]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00120]
−
−	* '''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=pdxT_19968_20558_1 pdxT] {{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:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1683 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3958 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 749 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 443 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 55 {{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>15911615,14762015,14651647 16030023, 19152323,17159152 23832367 25473090</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 63: / Line 63: @@
 === Additional information===
 =The protein=
@@ Line 90: / Line 87: @@
 * '''[[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 149: / Line 146: @@
 =References=
-<pubmed>15911615,14762015,14651647 16030023, 19152323,17159152 23832367 </pubmed>
+<pubmed>15911615,14762015,14651647 16030023, 19152323,17159152 23832367 25473090</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 126: / Line 126: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 1683 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 3958 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

← Older revision		Revision as of 09:38, 17 April 2014
Line 124:		Line 124:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1683 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3958 {{PubMed\|24696501}}

	=Biological materials =		=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=PdxT PdxT]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 4.984

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaDE.html]
@@ Line 92: / Line 93: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=BSU00120 pdxT]
 |-
-|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/PdxT PdxT]
+|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=PdxT PdxT]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 4.984

@@ Line 94: / Line 94: @@
 * '''Structure:'''
-** PdxT [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=43149 2NV0]
+** PdxT [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=43149 2NV0] {{PubMed|17159152}}
-** [[PdxS]]-[[PdxT]] complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=43151 2NV2]
+** [[PdxS]]-[[PdxT]] complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=43151 2NV2] {{PubMed|17159152}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P37528 P37528]

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 97: / Line 93: @@
 === Database entries ===
-* '''Structure:''' PdxT [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=43149 2NV0], [[PdxS]]-[[PdxT]] complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=43151 2NV2]
+* '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P37528 P37528]
@@ Line 109: / Line 107: @@
 =Expression and regulation=
-* '''Operon:''' ''[[pdxS]]-[[pdxT]]''
+* '''Operon:''' ''[[pdxS]]-[[pdxT]]'' {{PubMed|22383849}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdxT_19968_20558_1 pdxT] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:''' negatively controlled by [[Spo0A]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
@@ Line 143: / Line 141: @@
 =References=
-<pubmed>15911615,14762015,14651647 16030023, 19152323,17159152  </pubmed>
+<pubmed>15911615,14762015,14651647 16030023, 19152323,17159152 23832367 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=pdxT_19968_20558_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pdxT_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pdxT_19968_20558_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pdxT_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00120]]
 |-
 |}