YaaR - Revision history

Jgundlach: /* Biological materials */

2015-04-01T11:31:08Z

‎Biological materials

Jgundlach: /* Biological materials */

2015-04-01T11:24:30Z

‎Biological materials

Jstuelk at 19:00, 1 February 2015

2015-02-01T19:00:16Z

Jstuelk at 12:57, 10 November 2014

2014-11-10T12:57:21Z

134.76.38.147 at 12:45, 2 April 2014

2014-04-02T12:45:43Z

Jstuelk at 12:00, 14 March 2014

2014-03-14T12:00:15Z

Jstuelk: /* Database entries */

2013-12-05T11:56:15Z

‎Database entries

Jstuelk: /* Database entries */

2013-12-05T11:54:46Z

‎Database entries

Jstuelk at 11:26, 27 November 2013

2013-11-27T11:26:08Z

134.76.70.252 at 12:17, 16 May 2013

2013-05-16T12:17:42Z

← Older revision		Revision as of 11:31, 1 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' unknown <br/><br/>~~	+	{{#bank: YaaR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yaaR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| unknown~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| unknown~~
−	\|-
−	\|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=BSU00300 yaaR]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 16 kDa, 9.715~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 438 bp, 146 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[darA]]'', ''[[holB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00300 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00300 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00300 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yaaR_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=yaaR_40213_40653_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yaaR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00300]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[proteins of unknown function]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00300
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00300&redirect=T BSU00300]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10094]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''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=BSU00300&redirect=T BSU00300]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2qup 2QUP] (from ''Bacillus halodurans'', 40% identity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37539 P37539]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00300]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[darA]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaR_40213_40653_1 yaaR] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP1713 (''[[yaaQ]]-[[yaaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
−	** BKE00300 (''[[yaaR]]''::''erm'', available in the BGSC and in [[Jörg Stülke]]'s lab)
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed> 22383849</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 125: / Line 125: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:'''
+* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
 * '''Antibody:'''

@@ Line 117: / Line 117: @@
 * '''Mutant:'''
 ** GP1713 (''[[yaaQ]]-[[yaaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''

@@ Line 20: / Line 20: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 438 bp, 146 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaQ]]'', ''[[holB]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[darA]]'', ''[[holB]]''
 |-
 |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00300 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00300 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00300 DNA_with_flanks]
@@ Line 101: / Line 101: @@
 =Expression and regulation=
-* '''Operon:''' ''[[yaaQ]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}
+* '''Operon:''' ''[[darA]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaR_40213_40653_1 yaaR] {{PubMed|22383849}}

@@ Line 52: / Line 52: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 86: / Line 87: @@
 === Database entries ===
 * '''Structure:'''	[http://www.pdb.org/pdb/explore/explore.do?structureId=2qup 2QUP] (from ''Bacillus halodurans'', 40% identity)

@@ Line 58: / Line 58: @@
 === Additional information===
 =The protein=
@@ Line 76: / Line 73: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 106: / Line 103: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaR_40213_40653_1 yaaR] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 117: / Line 114: @@
 * '''Mutant:'''
 * '''Expression vector:'''

@@ Line 90: / Line 90: @@
 === Database entries ===
-* '''Structure:'''	[http://www.pdb.org/pdb/explore/explore.do?structureId=2qup 2QUP] (from ''Bacillus halodurans'')
+* '''Structure:'''	[http://www.pdb.org/pdb/explore/explore.do?structureId=2qup 2QUP] (from ''Bacillus halodurans'', 40% identity)
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P37539 P37539]

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 106: / Line 102: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''' ''[[yaaQ]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaR_40213_40653_1 yaaR] {{PubMed|22383849}}
@@ Line 137: / Line 133: @@
 =References=
+<pubmed> 22383849</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 27: / Line 27: @@
   <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=yaaR_40213_40653_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaR_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaR_40213_40653_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00300]]
 |-
 |}