YdaO - Revision history

Jstuelk: /* References */

2015-04-17T16:06:11Z

‎References

Jstuelk: /* References */

2014-08-05T08:12:40Z

‎References

134.76.38.147 at 13:01, 2 April 2014

2014-04-02T13:01:05Z

Jstuelk: /* Expression and regulation */

2013-12-14T17:30:48Z

‎Expression and regulation

Jstuelk at 17:08, 14 December 2013

2013-12-14T17:08:09Z

Jstuelk at 19:10, 28 November 2013

2013-11-28T19:10:59Z

Jstuelk: /* Basic information/ Evolution */

2013-11-28T18:59:23Z

‎Basic information/ Evolution

Fabian Commichau: /* Biological materials */

2013-08-01T20:58:02Z

‎Biological materials

Jstuelk: /* Biological materials */

2013-08-01T14:02:25Z

‎Biological materials

134.76.70.252 at 12:35, 16 May 2013

2013-05-16T12:35:03Z

← Older revision		Revision as of 16:06, 17 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' putative transporter <br/><br/>~~	+	{{#bank: YdaO}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ydaO''~~
−	\|-
−	~~\|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=BSU04320 ydaO]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 66 kDa, 9.929~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1821 bp, 607 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ydaN]]'', ''[[mutT]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU04320 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU04320 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU04320 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ydaO_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=ydaO_486432_488255_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ydaO_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU04320]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~{{SubtiWiki category\|[[proteins of unknown function]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[YdaO riboswitch]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU04320
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU04320&redirect=T BSU04320]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12062]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−	** [[APC superfamily of transport proteins\|amino acid, polyamine, organocation (APC) superfamily of transporters]], [http://www.tcdb.org/search/result.php?tc=2.A.3 TC 2.A.3]
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** cell membrane (according to [http://www.uniprot.org/uniprot/P96589 UniProt])
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU04320&redirect=T BSU04320]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P96589 P96589]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04320]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ydaO]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaO_486432_488255_1 ydaO] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** expression is controlled via termination antitermination by the [[ydaO riboswitch]], expression is switched off upon binding od c-di-AMP {{PubMed\|24141192,20511502}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A688 (''ydaO''::''erm''), {{PubMed\| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A688&Search=1A688 BGSC]
−	** GP93 (D''[[ydaO]]''::''cat''), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion: available in [[Fabian Commichau]]'s lab'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>15096624,20511502, 23086297 24141192 25086509 25086507 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 140: / Line 140: @@
 =References=
-<pubmed>15096624,20511502, 23086297 24141192</pubmed>
+<pubmed>15096624,20511502, 23086297 24141192 25086509 25086507 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 53: / Line 53: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 90: / Line 91: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 103: / Line 103: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''' ''[[ydaO]]'' {{PubMed|22383849}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaO_486432_488255_1 ydaO] {{PubMed|22383849}}

@@ Line 76: / Line 76: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 107: / Line 107: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaO_486432_488255_1 ydaO] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
 * '''Regulatory mechanism:'''
-** expression is controlled via termination antitermination by the [[ydaO riboswitch]] {{PubMed|23086297,20511502}}
+** expression is controlled via termination antitermination by the [[ydaO riboswitch]], expression is switched off upon binding od c-di-AMP {{PubMed|24141192,20511502}}
 * '''Additional information:'''
@@ Line 139: / Line 138: @@
 =References=
-<pubmed>15096624,20511502, 23086297 </pubmed>
+<pubmed>15096624,20511502, 23086297 24141192</pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 19:10, 28 November 2013
Line 1:		Line 1:
−	* '''Description:''' ~~unknown~~ <br/><br/>	+	* '''Description:''' putative transporter <br/><br/>

	{\| align="right" border="1" cellpadding="2"		{\| align="right" border="1" cellpadding="2"

← Older revision		Revision as of 18:59, 28 November 2013
Line 68:		Line 68:

	* '''Protein family:'''		* '''Protein family:'''
		+	** [[APC superfamily of transport proteins\|amino acid, polyamine, organocation (APC) superfamily of transporters]], [http://www.tcdb.org/search/result.php?tc=2.A.3 TC 2.A.3]

	* '''Paralogous protein(s):'''		* '''Paralogous protein(s):'''

@@ Line 119: / Line 119: @@
 * '''Mutant:'''
-** 1A688 ( ''ydaO''::''erm''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A688&Search=1A688 BGSC]
+** 1A688 (''ydaO''::''erm''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A688&Search=1A688 BGSC]
 ** GP93 (D''[[ydaO]]''::''cat''), available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''
-* '''lacZ fusion:'''
+* '''lacZ fusion: available in [[Fabian Commichau]]'s lab'''
 * '''GFP fusion:'''

@@ 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=ydaO_486432_488255_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ydaO_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaO_486432_488255_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ydaO_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU04320]]
 |-
 |}