FadB - Revision history

134.76.70.252 at 14:20, 17 April 2014

2014-04-17T14:20:56Z

134.76.70.252 at 09:48, 17 April 2014

2014-04-17T09:48:53Z

134.76.38.147 at 14:27, 2 April 2014

2014-04-02T14:27:14Z

134.76.70.252 at 11:24, 7 January 2014

2014-01-07T11:24:20Z

134.76.70.252 at 14:12, 16 May 2013

2013-05-16T14:12:55Z

134.76.70.252 at 10:56, 14 May 2013

2013-05-14T10:56:44Z

134.76.70.252 at 13:31, 13 May 2013

2013-05-13T13:31:52Z

134.76.70.252 at 09:05, 19 September 2012

2012-09-19T09:05:21Z

Jstuelk: /* Expression and regulation */

2012-08-23T15:44:15Z

‎Expression and regulation

134.76.70.252 at 14:40, 7 August 2012

2012-08-07T14:40:03Z

← Older revision		Revision as of 14:20, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' 3-hydroxyacyl-CoA dehydratase <br/><br/>~~	+	{{#bank: FadB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''fadB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ysiB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| 3-hydroxyacyl-CoA dehydratase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| fatty acid degradation~~
−	\|-
−	\|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=BSU28540 fadB]
−	\|-
−	\|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=fadB fadB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 27 kDa, 4.951~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 774 bp, 258 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[etfB]]'', ''[[fadR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28540 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28540 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28540 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ysiB_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=fadB_2917166_2917942_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:fadB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28540]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<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\|[[utilization of lipids]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CcpA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[FadR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU28540
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28540&redirect=T BSU28540]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lcfA-ysiAB-etfBA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12331]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H<sub>2</sub>O (according to Swiss-Prot)
−
−	* '''Protein family:''' enoyl-CoA hydratase/isomerase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−	** phosphorylated on Arg-230 {{PubMed\|22517742}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28540&redirect=T BSU28540]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=3PEA 3PEA] (from ''B. anthracis'', 49% identity, 66% similarity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P94549 P94549]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28540]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.17 4.2.1.17]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:'''
−	** ''[[lcfA]]-[[fadR]]-[[fadB]]-[[etfB]]-[[etfA]]'' {{PubMed\|17189250}}
−	** ''[[fadR]]-[[fadB]]-[[etfB]]-[[etfA]]'' {{PubMed\|17189250}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fadB_2917166_2917942_-1 fadB] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−	** ''[[lcfA]]'': [[SigA]] {{PubMed\|21398533}}
−	** ''[[fadR]]'': [[SigA]] {{PubMed\|17189250}}
−
−	* '''Regulation:'''
−	** induced by long-chain fatty acids ([[FadR]]) {{PubMed\|17189250}}
−	** subject to carbon catabolite repression (3.8-fold) ([[CcpA]]-[[PtsH\|HPr(Ser-P)]] {{PubMed\|12850135,21398533}}
−
−	* '''Regulatory mechanism:'''
−	** [[FadR]]: transcription repression {{PubMed\|17189250}}
−	** [[CcpA]]-[[PtsH\|HPr(Ser-P)]]: transcription repression {{PubMed\|21398533}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 165 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 665 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A854 ( ''fadB''::''cat''), {{PubMed\|17085570}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A854&Search=1A854 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~'''Additional publications:''' {{PubMed\|21398533}}~~
−	~~<pubmed>12850135, 17189250, 17919287 22517742</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:48, 17 April 2014
Line 131:		Line 131:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 165 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 665 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 60: / Line 60: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lcfA-ysiAB-etfBA.html]
@@ Line 98: / Line 99: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=3PEA 3PEA] (from ''B. anthracis'', 49% identity, 66% similarity)

@@ 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=BSU28540 fadB]
 |-
-|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_deg.html Fatty acid degradation]'''
+|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=fadB fadB]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 4.951

@@ 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=fadB_2917166_2917942_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:fadB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fadB_2917166_2917942_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:fadB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28540]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[etfB]]'', ''[[fadR]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28540 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28540 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28540 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28540 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28540 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28540 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ysiB_context.gif]]

← Older revision		Revision as of 09:05, 19 September 2012
Line 133:		Line 133:

	* '''Mutant:'''		* '''Mutant:'''
		+	** 1A854 ( ''fadB''::''cat''), {{PubMed\|17085570}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A854&Search=1A854 BGSC]

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

← Older revision		Revision as of 15:44, 23 August 2012
Line 117:		Line 117:

	* '''Sigma factor:'''		* '''Sigma factor:'''
		+	** ''[[lcfA]]'': [[SigA]] {{PubMed\|21398533}}
	** ''[[fadR]]'': [[SigA]] {{PubMed\|17189250}}		** ''[[fadR]]'': [[SigA]] {{PubMed\|17189250}}

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid degradation
 |-
 |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_deg.html Fatty acid degradation]'''