BkdR - Revision history

Jstuelk at 16:41, 30 August 2015

2015-08-30T16:41:29Z

Jstuelk: /* Extended information on the protein */

2014-10-27T16:10:32Z

‎Extended information on the protein

134.76.38.147 at 14:10, 2 April 2014

2014-04-02T14:10:07Z

134.76.70.252 at 11:10, 7 January 2014

2014-01-07T11:10:16Z

134.76.70.252 at 08:48, 12 November 2013

2013-11-12T08:48:26Z

134.76.70.252 at 13:51, 16 May 2013

2013-05-16T13:51:48Z

134.76.70.252 at 10:40, 14 May 2013

2013-05-14T10:40:30Z

134.76.70.252 at 13:14, 13 May 2013

2013-05-13T13:14:49Z

Jstuelk at 16:07, 12 November 2012

2012-11-12T16:07:00Z

134.76.70.252 at 12:04, 19 September 2012

2012-09-19T12:04:41Z

← 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 the ''[[ptb]]-[[bcd]]-[[buk]]-[[lpdV]]-[[bkdAA]]-[[bkdAB]]-[[bkdB]]'' operon <br/><br/>~~	+	{{#bank: BkdR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''bkdR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yqiR ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[transcription factors activating transcription at SigL-dependent promoters \|transcriptional activator]] (for [[SigL]]-dependent promoter))
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of branched-chain amino acid utilization,~~
−	~~required for survival at low temperatures)~~
−	\|-
−	\|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=BSU24100 bkdR]
−	~~required for survival at low temperatures)~~
−	\|-
−	\|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=BkdR BkdR]
−	\|-
−	\|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=bkdR bkdR]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 77 kDa, 6.237~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2076 bp, 692 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ptb]]'', ''[[yqzF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24100 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:bkdR_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=bkdR_2504789_2506867_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:bkdR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24100]]
−	\|-
−	\|}
−
−	~~__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]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}}~~
−	~~=The [[BkdR regulon]]:=~~
−	* ''[[ptb]]-[[bcd]]-[[buk]]-[[lpdV]]-[[bkdAA]]-[[bkdAB]]-[[bkdB]]''
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU24100
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~The mutant is cold-sensitive [http://www.ncbi.nlm.nih.gov/sites/entrez/16585774 PubMed]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24100&redirect=T BSU24100]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/bkdR.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11721]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−	** [[PAS domain]]
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:''' [[BkdR]]-[[SigL]] (activation)
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24100&redirect=T BSU24100]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P54529 P54529]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24100]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''bkdR'' {{PubMed\|12823818}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=bkdR_2504789_2506867_-1 bkdR] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−	** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094682 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10094682 PubMed]
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A913 ( ''bkdR''::''kan''), {{PubMed\|16585774}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A913&Search=1A913 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>16585774,10094682, 23123912,12823818 , </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 88: / Line 88: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''

@@ Line 63: / Line 63: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/bkdR.html]
@@ Line 100: / Line 101: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 20: / Line 20: @@
 |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=BkdR BkdR]
 |-
-|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/fatty_acid_synthesis.html Lipid synthesis]'''
+|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=bkdR bkdR]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 77 kDa, 6.237

@@ Line 18: / Line 18: @@
 required for survival at low temperatures)
 |-
-|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/BkdR BkdR]
+|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=BkdR BkdR]
 |-
 |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/fatty_acid_synthesis.html Lipid synthesis]'''

@@ Line 33: / Line 33: @@
   <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=bkdR_2504789_2506867_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:bkdR_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=bkdR_2504789_2506867_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:bkdR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24100]]
 |-
 |}

@@ Line 28: / Line 28: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ptb]]'', ''[[yqzF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24100 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24100 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:bkdR_context.gif]]

@@ Line 41: / Line 41: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 152: / Line 148: @@
 =References=
-<pubmed>16585774,10094682,,12823818 , </pubmed>
+<pubmed>16585774,10094682, 23123912,12823818 , </pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 12:04, 19 September 2012
Line 134:		Line 134:

	* '''Mutant:'''		* '''Mutant:'''
		+	** 1A913 ( ''bkdR''::''kan''), {{PubMed\|16585774}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A913&Search=1A913 BGSC]

	* '''Expression vector:'''		* '''Expression vector:'''