YdaP - Revision history

Jstuelk: /* Biological materials */

2015-06-12T14:55:59Z

‎Biological materials

134.76.38.147 at 13:01, 2 April 2014

2014-04-02T13:01:08Z

Jstuelk at 10:31, 20 August 2013

2013-08-20T10:31:18Z

134.76.70.252 at 12:35, 16 May 2013

2013-05-16T12:35:07Z

134.76.70.252 at 09:30, 14 May 2013

2013-05-14T09:30:39Z

134.76.70.252 at 12:10, 13 May 2013

2013-05-13T12:10:27Z

Jstuelk at 17:19, 23 August 2012

2012-08-23T17:19:54Z

Jstuelk at 16:55, 21 August 2012

2012-08-21T16:55:33Z

Jstuelk at 16:50, 21 August 2012

2012-08-21T16:50:59Z

Jstuelk: Undo revision 173296 by 91.201.64.26 (talk)

2012-08-21T16:47:15Z

Undo revision 173296 by 91.201.64.26 (talk)

← Older revision		Revision as of 14:55, 12 June 2015
Line 1:		Line 1:
−	* '''Description:~~''' general stress protein, required for survival of ethanol stress, putative pyruvate oxidase <br/><br/>~~	+	{{#bank: YdaP}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ydaP''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| putative pyruvate oxidase~~
−	\|-
−	~~\|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=BSU04340 ydaP]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 62 kDa, 5.217~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1722 bp, 574 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[mutT]]'', ''[[ydzK]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU04340 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU04340 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU04340 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ydaP_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=ydaP_488830_490554_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ydaP_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU04340]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[general stress proteins (controlled by SigB)]]}},~~
−	~~{{SubtiWiki category\|[[poorly characterized/ putative enzymes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigB regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU04340
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU04340&redirect=T BSU04340]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ydaP.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12063]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[AlsS]], [[IlvB]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU04340&redirect=T BSU04340]
−
−	* '''Structure:'''
−	** [http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=4KGD 4KGD] (the enzyme from Lactobacillus plantarum, 37% identity, 70% similarity) {{PubMed\|23748673}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P96591 P96591]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04340]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''ydaP'' {{PubMed\|10220166}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaP_488830_490554_1 ydaP] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
−	* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP457 (spc), available in [[Stülke]] lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>10220166, 23748673,15805528, 22730460 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 53: / Line 53: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ydaP.html]
@@ Line 87: / Line 88: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 89: / Line 89: @@
 * '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P96591 P96591]
@@ Line 104: / Line 105: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaP_488830_490554_1 ydaP] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 * '''Regulation:'''  induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
@@ Line 132: / Line 133: @@
 =References=
-<pubmed>10220166,,15805528, </pubmed>
+<pubmed>10220166, 23748673,15805528, 22730460 </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=ydaP_488830_490554_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ydaP_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaP_488830_490554_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ydaP_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU04340]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mutT]]'', ''[[ydzK]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU04340 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU04340 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU04340 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU04340 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU04340 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU04340 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ydaP_context.gif]]

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU04340 ydaP]
+|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=BSU04340 ydaP]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.217
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mutT]]'', ''[[ydzK]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12241&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU04340 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU04340 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU04340 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ydaP_context.gif]]

← Older revision		Revision as of 17:19, 23 August 2012
Line 1:		Line 1:
−	* '''Description:''' general stress protein, required for survival of ethanol stress, ~~similar to actolactate synthase~~	+	* '''Description:''' general stress protein, required for survival of ethanol stress, putative pyruvate oxidase <br/><br/>

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

@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || putative glyoxalate carboligase
+|style="background:#ABCDEF;" align="center"| '''Product''' || putative pyruvate oxidase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of glycolate and glyoxylate
+|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU04340 ydaP]

@@ Line 1: / Line 1: @@
 {| align="right" border="1" cellpadding="2"
@@ Line 34: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 62: / Line 59: @@
 === Additional information===
 =The protein=
@@ Line 74: / Line 68: @@
 * '''Protein family:'''
-* '''Paralogous protein(s):'''
+* '''Paralogous protein(s):''' [[AlsS]], [[IlvB]]
 === Extended information on the protein ===

← Older revision		Revision as of 16:47, 21 August 2012
Line 1:		Line 1:
−	~~SNsopd~~ <~~a href~~="http://~~ohifoairszfj~~.~~com~~/">~~ohifoairszfj~~</a>, [~~url~~=http://~~qwuwzotzbdmt~~.~~com~~/]~~qwuwzotzbdmt~~[/~~url~~], [~~link~~=http://~~jztsqfdvnvva~~.~~com~~/]~~jztsqfdvnvva~~[/~~link~~], http://~~aowtuvrqsbfy~~.~~com~~/	+
		+	{\| align="right" border="1" cellpadding="2"
		+	\|-
		+	\|style="background:#ABCDEF;" align="center"\|'''Gene name'''
		+	\|''ydaP''
		+	\|-
		+	\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''
		+	\|-
		+	\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no
		+	\|-
		+	\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| putative glyoxalate carboligase
		+	\|-
		+	\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| utilization of glycolate and glyoxylate
		+	\|-
		+	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU04340 ydaP]
		+	\|-
		+	\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 62 kDa, 5.217
		+	\|-
		+	\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1722 bp, 574 aa
		+	\|-
		+	\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[mutT]]'', ''[[ydzK]]''
		+	\|-
		+	\|colspan="2" style="background:#FAF8CC;" align="center"\|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12241]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
		+	\|-
		+	\|colspan="2" \| '''Genetic context''' <br/> [[Image:ydaP_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=ydaP_488830_490554_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ydaP_expression.png\|500px]]
		+	\|-
		+	\|}
		+
		+	__TOC__
		+	<br/><br/><br/><br/>
		+	<br/><br/><br/><br/>
		+	<br/><br/><br/><br/>
		+	<br/><br/><br/><br/>
		+	<br/><br/><br/><br/>
		+
		+
		+	<br/><br/>
		+
		+	= [[Categories]] containing this gene/protein =
		+	{{SubtiWiki category\|[[general stress proteins (controlled by SigB)]]}},
		+	{{SubtiWiki category\|[[poorly characterized/ putative enzymes]]}}
		+
		+	= This gene is a member of the following [[regulons]] =
		+	{{SubtiWiki regulon\|[[SigB regulon]]}}
		+
		+	=The gene=
		+
		+	=== Basic information ===
		+
		+	* '''Locus tag:''' BSU04340
		+
		+	===Phenotypes of a mutant ===
		+
		+	=== Database entries ===
		+
		+	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ydaP.html]
		+
		+	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12063]
		+
		+	=== 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:'''
		+
		+	* '''Cofactor(s):'''
		+
		+	* '''Effectors of protein activity:'''
		+
		+	* '''[[SubtInteract\|Interactions]]:'''
		+
		+	* '''[[Localization]]:'''
		+
		+	=== Database entries ===
		+
		+	* '''Structure:'''
		+
		+	* '''UniProt:''' [http://www.uniprot.org/uniprot/P96591 P96591]
		+
		+	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04340]
		+
		+	* '''E.C. number:'''
		+
		+	=== Additional information===
		+
		+	=Expression and regulation=
		+
		+	* '''Operon:''' ''ydaP'' {{PubMed\|10220166}}
		+
		+	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydaP_488830_490554_1 ydaP] {{PubMed\|22383849}}
		+
		+	* '''Sigma factor:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
		+
		+	* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
		+
		+	* '''Regulatory mechanism:'''
		+
		+	* '''Additional information:'''
		+
		+	=Biological materials =
		+
		+	* '''Mutant:''' GP457 (spc), available in [[Stülke]] lab
		+
		+	* '''Expression vector:'''
		+
		+	* '''lacZ fusion:'''
		+
		+	* '''GFP fusion:'''
		+
		+	* '''two-hybrid system:'''
		+
		+	* '''Antibody:'''
		+
		+	=Labs working on this gene/protein=
		+
		+	=Your additional remarks=
		+
		+	=References=
		+
		+	<pubmed>10220166,,15805528, </pubmed>
		+
		+	[[Category:Protein-coding genes]]