YrhJ - Revision history

Jstuelk at 16:59, 16 February 2015

2015-02-16T16:59:46Z

134.76.70.252 at 11:48, 8 April 2014

2014-04-08T11:48:08Z

134.76.38.147 at 14:21, 2 April 2014

2014-04-02T14:21:04Z

Jstuelk: /* References */

2013-10-23T08:04:11Z

‎References

134.76.70.252 at 14:03, 16 May 2013

2013-05-16T14:03:27Z

134.76.70.252 at 10:50, 14 May 2013

2013-05-14T10:50:55Z

134.76.70.252 at 13:26, 13 May 2013

2013-05-13T13:26:01Z

Jstuelk at 08:22, 4 March 2013

2013-03-04T08:22:40Z

134.76.70.252 at 14:17, 7 August 2012

2012-08-07T14:17:51Z

134.76.70.252 at 09:48, 20 April 2012

2012-04-20T09:48:19Z

← Older revision		Revision as of 16:59, 16 February 2015
Line 1:		Line 1:
−	* '''Description:~~''' [[cytochrome P450]] (CYP102A3)/ NADPH-[[cytochrome P450]] reductase <br/><br/>~~	+	{{#bank: YrhJ}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yrhJ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''cypE ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| NADPH-[[cytochrome P450]] reductase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| fatty acid metabolism~~
−	\|-
−	\|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=BSU27160 yrhJ]
−	\|-
−	\|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=YrhJ YrhJ]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 118 kDa, 6.017~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 3162 bp, 1054 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[rrcM]]'', ''[[fatR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU27160 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU27160 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU27160 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yrhJ_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=cypB_2773890_2777054_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yrhJ_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU27160]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−
−
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[electron transport/ other]]}},~~
−	~~{{SubtiWiki category\|[[lipid metabolism/ other]]}},~~
−	~~{{SubtiWiki category\|[[cell envelope stress proteins (controlled by SigM, V, W, X, Y)]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[FatR regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigM regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigW regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigX regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU27160
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU27160&redirect=T BSU27160]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yrhIJ.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12299]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** hydroxylates medium-chain fatty acids in subterminal positions {{PubMed\|14741768}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[YetO]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** cell membrane (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU27160&redirect=T BSU27160]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2X7Y 2X7Y] (from Bacillus megaterium; 67% identity, 88% similarity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O08336 O08336]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27160]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.6.2.4 1.6.2.4]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:'''
−	** ''[[fatR]]-[[yrhJ]]'' {{PubMed\|10917605}}
−	** ''[[yrhH]]-[[fatR]]-[[yrhJ]]'' {{PubMed\|18179421}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cypB_2773890_2777054_-1 yrhJ] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigM]] {{PubMed\|12775685}}, [[SigW]] {{PubMed\|12207695}}, [[SigX]] {{PubMed\|9636707}}
−
−	* '''Regulation:'''
−	** induced by unsaturated fatty acids ([[FatR]]) {{PubMed\|11734890}}
−	** expression is reduced in a [[SigV]] mutant {{PubMed\|21926231}}
−
−	* '''Regulatory mechanism:'''
−	** [[FatR]]: transcription repression {{PubMed\|11734890}}
−
−	* '''Additional information:'''
−	** A [[ncRNA]] is predicted between ''[[yrhK]]'' and ''[[yrhJ]]'' {{PubMed\|20525796}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>11734890,10917605 ,11574077,14741768,15122913, 12775685 16716428 16381045 20525796 12207695 9636707 21926231</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 15: / Line 15: @@
 |-
 |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=BSU27160 yrhJ]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 118 kDa, 6.017

@@ Line 62: / Line 62: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yrhIJ.html]
@@ Line 98: / Line 99: @@
 === Database entries ===
 * '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2X7Y 2X7Y] (from Bacillus megaterium; 67% identity, 88% similarity)

@@ Line 147: / Line 147: @@
 =References=
-'''Additional publications:''' {{PubMed|21926231}}
+<pubmed>11734890,10917605 ,11574077,14741768,15122913, 12775685 16716428 16381045 20525796 12207695 9636707 21926231</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=cypB_2773890_2777054_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yrhJ_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cypB_2773890_2777054_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yrhJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU27160]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rrcM]]'', ''[[fatR]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU27160 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU27160 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU27160 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU27160 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU27160 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU27160 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yrhJ_context.gif]]

@@ Line 20: / Line 20: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3162 bp, 1054 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrhK]]'', ''[[fatR]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rrcM]]'', ''[[fatR]]''
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14658&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid metabolism
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 118 kDa, 6.017