YerD - Revision history

Jstuelk: /* Additional information */

2015-04-15T17:43:57Z

‎Additional information

Jstuelk: /* Additional information */

2015-04-15T17:43:39Z

‎Additional information

134.76.38.147 at 13:08, 2 April 2014

2014-04-02T13:08:29Z

Jstuelk at 19:31, 15 September 2013

2013-09-15T19:31:09Z

Jstuelk: /* References */

2013-06-04T11:13:59Z

‎References

134.76.70.252 at 12:42, 16 May 2013

2013-05-16T12:42:56Z

134.76.70.252 at 09:38, 14 May 2013

2013-05-14T09:38:14Z

134.76.70.252 at 12:17, 13 May 2013

2013-05-13T12:17:53Z

Jstuelk at 19:16, 8 October 2012

2012-10-08T19:16:38Z

Fabian Commichau: /* Labs working on this gene/protein */

2012-09-18T19:10:10Z

‎Labs working on this gene/protein

← Older revision		Revision as of 17:43, 15 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' general stress protein, similar to glutamate synthase (ferredoxin), required for protection against paraquat stress <br/><br/>~~	+	{{#bank: YerD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yerD''~~
−	\|-
−	~~\|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''' \|\| protection against paraquat stress~~
−	\|-
−	\|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=BSU06590 yerD]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 58 kDa, 7.349~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1575 bp, 525 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yerC]]'', ''[[pcrB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06590 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06590 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06590 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yerD_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=yerD_716780_718357_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yerD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU06590]]
−	\|-
−	\|}
−
−	~~__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\|[[resistance against oxidative and electrophile stress]]}},~~
−	~~{{SubtiWiki category\|[[poorly characterized/ putative enzymes]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigB regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU06590
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU06590&redirect=T BSU06590]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12832]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[GltA]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** cell membrane (according to UniProt)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU06590&redirect=T BSU06590]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34849 O34849]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06590]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−	~~Schreib~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[yerD]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yerD_716780_718357_-1 yerD] {{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]
−	** strongly induced in response to glucose starvation in M9 medium {{PubMed\|23033921}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP1184 (tet) available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:''' pBP32 (expression vector for ''E. coli'' BL21; N-terminal Strep-tag-YerD fusion protein, based on [[pGP172]]), available in [[Fabian Commichau]]'s lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''FLAG-tag construct:''' GP1187 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Fabian_Commichau\|Fabian Commichau]] University of Göttingen, Germany~~
−	~~[http://genmibio.uni-goettingen.de/index.php?id=130 Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>15805528, 22383849 23033921 22582280</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 17:43, 15 April 2015
Line 105:		Line 105:

	=== Additional information===		=== Additional information===
		+	Schreib

	=Expression and regulation=		=Expression and regulation=

@@ Line 55: / Line 55: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 1: / Line 1: @@
-* '''Description:''' general stress protein, similar to glutamate synthase (ferredoxin) <br/><br/>
+* '''Description:''' general stress protein, similar to glutamate synthase (ferredoxin), required for protection against paraquat stress  <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+|style="background:#ABCDEF;" align="center"|'''Function''' || protection against paraquat stress
 |-
 |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=BSU06590 yerD]
@@ Line 39: / Line 39: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
 {{SubtiWiki category|[[poorly characterized/ putative enzymes]]}},
 {{SubtiWiki category|[[membrane proteins]]}}
@@ Line 109: / Line 110: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yerD_716780_718357_-1 yerD] {{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:'''
@@ Line 143: / Line 144: @@
 =References=
-<pubmed>15805528, 22383849 23033921</pubmed>
+<pubmed>15805528, 22383849 23033921 22582280</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 143: / Line 143: @@
 =References=
-'''Additional publications:''' {{PubMed|23033921}}
+<pubmed>15805528, 22383849 23033921</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=yerD_716780_718357_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yerD_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yerD_716780_718357_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yerD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU06590]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yerC]]'', ''[[pcrB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06590 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06590 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06590 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06590 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06590 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06590 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yerD_context.gif]]

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 115: / Line 111: @@
 * '''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]
+* '''Regulation:'''
 * '''Regulatory mechanism:'''
@@ Line 145: / Line 143: @@
 =References=
+'''Additional publications:''' {{PubMed|23033921}}
 <pubmed>15805528, 22383849</pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 19:10, 18 September 2012
Line 138:		Line 138:

	=Labs working on this gene/protein=		=Labs working on this gene/protein=
		+
		+	[[Fabian_Commichau\|Fabian Commichau]] University of Göttingen, Germany
		+	[http://genmibio.uni-goettingen.de/index.php?id=130 Homepage]

	=Your additional remarks=		=Your additional remarks=