ValS - Revision history

Jstuelk: /* Original Publications */

2014-10-20T15:32:13Z

‎Original Publications

134.76.70.252 at 09:44, 17 April 2014

2014-04-17T09:44:01Z

134.76.38.147 at 14:24, 2 April 2014

2014-04-02T14:24:46Z

Jstuelk at 16:41, 5 March 2014

2014-03-05T16:41:10Z

134.76.70.252 at 11:22, 7 January 2014

2014-01-07T11:22:27Z

134.76.70.252 at 14:10, 16 May 2013

2013-05-16T14:10:37Z

134.76.70.252 at 10:54, 14 May 2013

2013-05-14T10:54:26Z

134.76.70.252 at 13:29, 13 May 2013

2013-05-13T13:29:39Z

Jstuelk at 19:25, 29 April 2013

2013-04-29T19:25:02Z

Awiechert at 09:16, 5 December 2012

2012-12-05T09:16:05Z

← Older revision		Revision as of 15:32, 20 October 2014
Line 1:		Line 1:
−	* '''Description:~~''' valyl-tRNA synthetase <br/><br/>~~	+	{{#bank: ValS}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''valS''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| valyl-tRNA synthetase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[translation]]~~
−	\|-
−	\|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=BSU28090 valS]
−	\|-
−	\|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=valS valS]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 101 kDa, 4.868~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2640 bp, 880 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[folC]]'', ''[[yszA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28090 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:valS_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=valS_2866664_2869306_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:valS_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28090]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[translation]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[T-box]]}},~~
−	~~[[Efp-dependent proteins]]~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU28090
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28090&redirect=T BSU28090]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/valS-folC.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10321]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val) (according to Swiss-Prot)
−
−	* '''Protein family:''' ValS type 1 subfamily (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28090&redirect=T BSU28090]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1IYW 1IYW] (from ''Thermus thermophilus'', 41% identity, 60% similarity) {{PubMed\|12554880}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/Q05873 Q05873]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28090]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.9 6.1.1.9]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[valS]]-[[folC]]'' {{PubMed\|9098041}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=valS_2866664_2869306_-1 valS] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|9098041}}
−
−	* '''Regulation:'''
−	** induced by valine limitation ([[T-box]]) {{PubMed\|9098041,19258532}}
−
−	* '''Regulatory mechanism:'''
−	** [[T-box]]: [[riboswitch]], transcription termination/antitermination {{PubMed\|9098041,19258532}}
−
−	* '''Additional information:'''
−	** [[translation]] is likely to require [[Efp]] due to the presence of several consecutive proline residues {{PubMed\|23239624,23239623}}
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1169 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3552 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>19258532,, </pubmed>~~
−	~~==Original Publications==~~
−	~~<pubmed>,9098041, 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 125: / Line 125: @@
 ** [[translation]] is likely to require [[Efp]] due to the presence of several consecutive proline residues {{PubMed|23239624,23239623}}
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 61: / Line 61: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/valS-folC.html]
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1IYW 1IYW] (from ''Thermus thermophilus'', 41% identity, 60% similarity) {{PubMed|12554880}}

@@ Line 43: / Line 43: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[translation]]}},
-{{SubtiWiki category|[[essential genes]]}}
+{{SubtiWiki category|[[essential genes]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 66: / Line 67: @@
 === Additional information===
 =The protein=
@@ Line 84: / Line 82: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 124: / Line 122: @@
 * '''Additional information:'''
 ** [[translation]] is likely to require [[Efp]] due to the presence of several consecutive proline residues {{PubMed|23239624,23239623}}
 =Biological materials =
@@ Line 147: / Line 146: @@
 <pubmed>19258532,, </pubmed>
 ==Original Publications==
-<pubmed>,9098041, </pubmed>
+<pubmed>,9098041, 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=BSU28090 valS]
 |-
-|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/tRNA_charging.html tRNA charging], [http://subtiwiki.uni-goettingen.de/pathways/folate_biosynthesis.html Folate]'''
+|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=valS valS]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 101 kDa, 4.868

@@ 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=valS_2866664_2869306_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:valS_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=valS_2866664_2869306_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:valS_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28090]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[folC]]'', ''[[yszA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28090 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28090 DNA_with_flanks]
 |-
 |-

@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || valyl-tRNA synthetase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || translation
+|style="background:#ABCDEF;" align="center"|'''Function''' || [[translation]]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU28090 valS]
@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 50: / Line 46: @@
 = This gene is a member of the following [[regulons]] =
-{{SubtiWiki regulon|[[T-box]]}}
+{{SubtiWiki regulon|[[T-box]]}},
 =The gene=
@@ Line 117: / Line 114: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=valS_2866664_2869306_-1 valS] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|9098041}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|9098041}}
 * '''Regulation:'''
@@ Line 126: / Line 123: @@
 * '''Additional information:'''
 =Biological materials =

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2640 bp, 880 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[folC]]'', ''[[ysxE]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[folC]]'', ''[[yszA]]''
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14769&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''