DeaD - Revision history

Jstuelk: /* References */

2015-04-26T15:23:00Z

‎References

134.76.70.252 at 09:58, 17 April 2014

2014-04-17T09:58:01Z

134.76.38.147 at 15:11, 2 April 2014

2014-04-02T15:11:06Z

134.76.70.252 at 09:42, 12 November 2013

2013-11-12T09:42:42Z

134.76.70.252 at 14:57, 16 May 2013

2013-05-16T14:57:20Z

134.76.70.252 at 11:39, 14 May 2013

2013-05-14T11:39:33Z

134.76.70.252 at 14:14, 13 May 2013

2013-05-13T14:14:02Z

Jstuelk at 08:50, 1 May 2013

2013-05-01T08:50:36Z

Jstuelk at 16:47, 26 November 2012

2012-11-26T16:47:16Z

Jstuelk at 12:59, 24 November 2012

2012-11-24T12:59:51Z

← Older revision		Revision as of 15:23, 26 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' [[DEAD-box RNA helicases\|DEAD-box RNA helicase]], important for adaptation to low temperatures<br/><br/>~~	+	{{#bank: DeaD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''deaD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yxiN ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[DEAD-box RNA helicases\|DEAD-box RNA helicase]]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| RNA helicase~~
−	\|-
−	\|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=BSU39110 deaD]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=DeaD DeaD]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 53 kDa, 7.706~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1437 bp, 479 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yxiO]]'', ''[[yxiM]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU39110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU39110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU39110 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:deaD_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=deaD_4015987_4017426_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:deaD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU39110]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[DEAD-box RNA helicases]]}},~~
−	~~{{SubtiWiki category\|[[translation]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU39110
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU39110&redirect=T BSU39110]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiM-deaD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11143]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** RNA helicase
−	** required for [[ribosome]] assembly {{PubMed\|23175651}}
−
−	* '''Protein family:''' [[DEAD-box RNA helicases\|DEAD-box RNA helicase]]
−
−	* '''Paralogous protein(s):''' [[CshA]], [[CshB]], [[YfmL]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−	**Helicase domain 1: AS 1-203
−	**Linker region: AS 204-212
−	**Helicase domain 2: AS 207-368
−	**RNA-binding domain: AS 404-479
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[DeaD]]-[[CshA]] {{PubMed\|20572937}}
−	** [[DeaD]]-[[CshB]] {{PubMed\|20572937}}
−	** [[DeaD]]-[[23S rRNA]] {{PubMed\|20673833}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU39110&redirect=T BSU39110]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2G0C 2G0C] (RNA-binding domain, AA 404-479), [http://www.rcsb.org/pdb/explore.do?structureId=2HJV 2HJV] (second domain, AA 207-368); [http://www.rcsb.org/pdb/explore/explore.do?pdbId=3MOJ 3MOJ] (RNA binding domain complexed with a fragment of 23S ribosomal RNA) {{PubMed\|20673833}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P42305 P42305]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39110]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[yxiM]]-[[deaD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=deaD_4015987_4017426_-1 deaD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** expression declines in the stationary phase {{PubMed\|23175651}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 96 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP1052 (tet), available in the [[Stülke]] lab
−
−	* '''Expression vector:'''
−	** for expression/ purification from ''B. subtilis'' with C-terminal Strep-tag, for [[SPINE]], expression from the native chromomsomal site: GP1065 (spc), available in [[Jörg Stülke]]'s lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
−
−	* '''FLAG-tag construct:'''
−	** GP1068 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Dagmar Klostermeier]], Biozentrum Basel, Switzerland [http://www.biozentrum.unibas.ch/klostermeier/index.html homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>17142894 16118224 17229151, 16611943 19839642 19474341 18184816 17951299 12460566 10481020 20572937 20673833 20691700 23175651 23625962 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:58, 17 April 2014
Line 127:		Line 127:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 96 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiM-deaD.html]
@@ Line 100: / Line 101: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2G0C 2G0C] (RNA-binding domain, AA 404-479),  [http://www.rcsb.org/pdb/explore.do?structureId=2HJV 2HJV] (second domain, AA 207-368); [http://www.rcsb.org/pdb/explore/explore.do?pdbId=3MOJ 3MOJ] (RNA binding domain complexed with a fragment of 23S ribosomal RNA) {{PubMed|20673833}}

@@ 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=BSU39110 deaD]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/DeaD DeaD]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=DeaD DeaD]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 7.706

@@ 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=deaD_4015987_4017426_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:deaD_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=deaD_4015987_4017426_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:deaD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU39110]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiO]]'', ''[[yxiM]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU39110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU39110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU39110 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU39110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU39110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU39110 DNA_with_flanks]
 |-
 |-

@@ Line 152: / Line 152: @@
 =References=
-<pubmed>17142894 16118224 17229151, 16611943 19839642 19474341 18184816 17951299 12460566 10481020 20572937 20673833 20691700 23175651</pubmed>
+<pubmed>17142894 16118224 17229151, 16611943 19839642 19474341 18184816 17951299 12460566 10481020 20572937 20673833 20691700 23175651 23625962 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 1: / Line 1: @@
-* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]]<br/><br/>
+* '''Description:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]], important for adaptation to low temperatures<br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 68: / Line 68: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:''' RNA helicase
+* '''Catalyzed reaction/ biological activity:'''
 * '''Protein family:''' [[DEAD-box RNA helicases|DEAD-box RNA helicase]]
@@ Line 118: / Line 120: @@
 * '''Regulation:'''
 * '''Regulatory mechanism:'''

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 67: / Line 63: @@
 === Additional information===
 =The protein=
@@ Line 122: / Line 115: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=deaD_4015987_4017426_-1 deaD] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 156: / Line 149: @@
 =References=
-<pubmed>17142894 16118224 17229151, 16611943 19839642 19474341 18184816 17951299 12460566 10481020 20572937 20673833 20691700 </pubmed>
+<pubmed>17142894 16118224 17229151, 16611943 19839642 19474341 18184816 17951299 12460566 10481020 20572937 20673833 20691700 23175651</pubmed>
 [[Category:Protein-coding genes]]