RapJ - Revision history

134.76.38.147 at 12:55, 2 April 2014

2014-04-02T12:55:32Z

134.76.70.252 at 15:08, 11 November 2013

2013-11-11T15:08:16Z

134.76.70.252 at 12:29, 16 May 2013

2013-05-16T12:29:09Z

134.76.70.252 at 09:24, 14 May 2013

2013-05-14T09:24:52Z

134.76.70.252 at 12:04, 13 May 2013

2013-05-13T12:04:55Z

Jstuelk at 17:41, 27 March 2013

2013-03-27T17:41:04Z

Jstuelk at 17:20, 27 March 2013

2013-03-27T17:20:16Z

134.76.70.252 at 09:28, 8 August 2012

2012-08-08T09:28:57Z

134.76.70.252 at 08:35, 8 August 2012

2012-08-08T08:35:36Z

134.76.70.252 at 15:19, 7 August 2012

2012-08-07T15:19:30Z

← Older revision		Revision as of 12:55, 2 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' [[response regulator aspartate phosphatase]], dephosphorylates [[Spo0F]]-P<br/><br/>~~	+	{{#bank: RapJ}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''rapJ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ycdE ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[response regulator aspartate phosphatase]]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of the [[phosphorelay]]~~
−	\|-
−	\|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=BSU02820 rapJ]
−	\|-
−	\|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=RapJ RapJ]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 44 kDa, 4.902~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1119 bp, 373 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[cwlK]]'', ''[[ycdF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02820 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02820 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02820 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:rapJ_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=rapJ_304430_305551_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:rapJ_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02820]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[protein modification]]}},~~
−	~~{{SubtiWiki category\|[[phosphorelay]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU02820
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rapJ.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12663]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** dephosphorylates [[Spo0F]]-P {{PubMed\|21346797}}
−
−	* '''Protein family:''' RAP family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−	** RapJ is made up of the C-terminal tetratricopeptide repeat (TPR) domain that is connected by a flexible helix containing linker to the N-terminal 3-helix bundle. Upon binding of the regulating peptide [[PhrC]], the 3-helix bundle and the linker helix undergo a conformational change to form a TPR-like fold that merges with the existing C-terminal TPR domain. {{PubMed\|23526881}}
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−	** the interaction with [[PhrC]] inactivates [[RapJ]] {{PubMed\|23526881}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[RapJ]]-[[Spo0F]], dephosphorylation of [[Spo0F]]-P {{PubMed\|21346797}}
−	** [[RapJ]]-[[PhrC]] {{PubMed\|23526881}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore/explore.do?structureId=4GYO 4GYO] (complex [[RapJ]]-[[PhrC]]) {{PubMed\|23526881}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34327 O34327]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU02820]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''rapJ'' (according to [http://dbtbs.hgc.jp/COG/prom/rapJ.html DBTBS])
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rapJ_304430_305551_1 rapJ] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>21346797 23526881 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ 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=BSU02820 rapJ]
 |-
-|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/RapJ RapJ]
+|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=RapJ RapJ]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 4.902

@@ Line 29: / Line 29: @@
   <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=rapJ_304430_305551_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rapJ_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rapJ_304430_305551_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rapJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02820]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cwlK]]'', ''[[ycdF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02820 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02820 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02820 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02820 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02820 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02820 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:rapJ_context.gif]]

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || control of the [[phosphorelay]]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU02820 rapJ]
+|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=BSU02820 rapJ]
 |-
 |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/RapJ RapJ]
@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cwlK]]'', ''[[ycdF]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12076&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02820 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02820 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02820 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:rapJ_context.gif]]

@@ Line 82: / Line 82: @@
 * '''Domains:'''
+** RapJ is made up of the C-terminal tetratricopeptide repeat (TPR) domain that is connected by a flexible helix containing linker to the N-terminal 3-helix bundle. Upon binding of the regulating peptide [[PhrC]], the 3-helix bundle and the linker helix undergo a conformational change to form a TPR-like fold that merges with the existing C-terminal TPR domain. {{PubMed|23526881}}
 * '''Modification:'''
@@ Line 99: / Line 99: @@
 * '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O34327 O34327]
@@ Line 114: / Line 115: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rapJ_304430_305551_1 rapJ] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''

@@ Line 1: / Line 1: @@
-* '''Description:''' [[response regulator aspartate phosphatase]]<br/><br/>
+* '''Description:''' [[response regulator aspartate phosphatase]], dephosphorylates [[Spo0F]]-P<br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || [[response regulator aspartate phosphatase]]
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+|style="background:#ABCDEF;" align="center"|'''Function''' || control of the [[phosphorelay]]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU02820 rapJ]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 4.902
@@ Line 35: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[protein modification]]}},
 {{SubtiWiki category|[[transcription factors and their control]]}}
@@ Line 72: / Line 71: @@
 * '''Catalyzed reaction/ biological activity:'''
 * '''Protein family:''' RAP family (according to Swiss-Prot)
@@ Line 88: / Line 88: @@
 * '''Effectors of protein activity:'''
 * '''[[SubtInteract|Interactions]]:'''
 * '''[[Localization]]:'''
@@ Line 134: / Line 137: @@
 =Labs working on this gene/protein=
 =Your additional remarks=
 =References=
+<pubmed>21346797 23526881 </pubmed>
 [[Category:Protein-coding genes]]