RocR - Revision history

Jstuelk: /* References */

2015-08-30T16:41:44Z

‎References

Jstuelk: /* Extended information on the protein */

2014-10-27T16:11:57Z

‎Extended information on the protein

134.76.38.147 at 15:16, 2 April 2014

2014-04-02T15:16:31Z

134.76.70.252 at 12:03, 7 January 2014

2014-01-07T12:03:53Z

134.76.70.252 at 09:47, 12 November 2013

2013-11-12T09:47:31Z

Jstuelk at 07:34, 23 July 2013

2013-07-23T07:34:52Z

134.76.70.252 at 15:01, 16 May 2013

2013-05-16T15:01:36Z

134.76.70.252 at 11:44, 14 May 2013

2013-05-14T11:44:17Z

134.76.70.252 at 14:19, 13 May 2013

2013-05-13T14:19:09Z

Awiechert at 13:34, 5 December 2012

2012-12-05T13:34:15Z

← Older revision		Revision as of 16:41, 30 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' [[transcription factors activating transcription at SigL-dependent promoters \|transcriptional activator]] of arginine utilization operons <br/><br/>~~	+	{{#bank: RocR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''rocR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[transcription factors activating transcription at SigL-dependent promoters \|transcriptional activator]]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| transcriptional activator of arginine utilization operons~~
−	\|-
−	\|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=BSU40350 rocR]
−	\|-
−	\|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=RocR RocR]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=rocR rocR]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 52.6 kDa, 6.08~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1383 bp, 461 amino acids~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[rocD]]'', ''[[yyzO]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40350 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40350 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40350 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:rocR_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=rocR_4145747_4147132_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:rocR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40350]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−
−	~~= [[Categories]] containing this gene/protein =~~
−	* {{SubtiWiki category\|[[utilization of amino acids]]}},
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}}~~
−	* see also: [[glutamate metabolism]]
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−	~~=The [[RocR regulon]]=~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU40350
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40350&redirect=T BSU40350]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocR.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10723]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' transcription activation at [[SigL]]-dependent promoters of ''[[rocA\|rocABC]]'', ''[[rocD\|rocDEF]]'', and ''[[rocG]]''
−
−	* '''Protein family:''' [[SigL \| Sigma-54]] interacting transcription activator
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−	** [[SigL \| Sigma-54]] factor interaction domain (143–372)
−	** 2x nucleotid-binding domain (171–178),(233–242)
−	** HTH motif (434–453)
−	** [[PAS domain]]
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):''' ornithine or citrulline are required for RocR-dependent transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/9194709 PubMed]
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** RocR-[[SigL]]
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40350&redirect=T BSU40350]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P38022 P38022]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40350]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''rocR'' (according to [http://dbtbs.hgc.jp/COG/prom/rocR.html DBTBS])
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rocR_4145747_4147132_1 rocR] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
−
−	* '''Regulation:''' autoregulation by [[RocR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
−
−	* '''Regulatory mechanism:''' autorepression
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' QB5533 (aphA3), from [[Michel Debarbouille]], available in [[Stülke]] lab
−	** 1A911 ( ''rocR''::''kan''), {{PubMed\|16585774}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A911&Search=1A911 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>12634342 8113162,9194709 21965396 23869754</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 82: / Line 82: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
-**[[SigL | Sigma-54]] factor interaction domain (143–372)
+** [[SigL | Sigma-54]] factor interaction domain (143–372)
-**2x nucleotid-binding domain (171–178),(233–242)
+** 2x nucleotid-binding domain (171–178),(233–242)
-**HTH motif (434–453)
+** HTH motif (434–453)
 * '''Modification:'''

@@ Line 60: / Line 60: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocR.html]
@@ Line 98: / Line 99: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 18: / Line 18: @@
 |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=RocR RocR]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=rocR rocR]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52.6 kDa, 6.08

@@ 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=BSU40350 rocR]
 |-
-|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/RocR RocR]
+|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=RocR RocR]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate]'''

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
@@ Line 117: / Line 113: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rocR_4145747_4147132_1 rocR] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
+* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
 * '''Regulation:''' autoregulation by [[RocR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
@@ Line 146: / Line 142: @@
 =References=
-<pubmed>12634342 8113162,9194709 21965396 </pubmed>
+<pubmed>12634342 8113162,9194709 21965396 23869754</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=rocR_4145747_4147132_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rocR_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rocR_4145747_4147132_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rocR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40350]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocD]]'', ''[[yyzO]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40350 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40350 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40350 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40350 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40350 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40350 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:rocR_context.gif]]

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1383 bp, 461 amino acids
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocD]]'', ''[[yyxA]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocD]]'', ''[[yyzO]]''
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16072&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''