DhbE - Revision history

Jstuelk: /* References */

2015-02-08T15:59:11Z

‎References

134.76.70.252 at 14:05, 17 April 2014

2014-04-17T14:05:37Z

134.76.70.252 at 09:24, 17 April 2014

2014-04-17T09:24:29Z

134.76.70.252 at 11:51, 8 April 2014

2014-04-08T11:51:41Z

134.76.38.147 at 14:39, 2 April 2014

2014-04-02T14:39:39Z

Jstuelk at 20:48, 18 June 2013

2013-06-18T20:48:28Z

134.76.70.252 at 14:28, 16 May 2013

2013-05-16T14:28:28Z

134.76.70.252 at 11:10, 14 May 2013

2013-05-14T11:10:23Z

134.76.70.252 at 13:45, 13 May 2013

2013-05-13T13:45:29Z

134.76.70.252 at 15:33, 7 August 2012

2012-08-07T15:33:43Z

← Older revision		Revision as of 15:59, 8 February 2015
Line 1:		Line 1:
−	* '''Description:~~''' 2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E) <br/><br/>~~	+	{{#bank: DhbE}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''dhbE''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''entE ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| 2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| biosynthesis of the siderophore bacillibactin~~
−	\|-
−	\|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=BSU31980 dhbE]
−	\|-
−	\|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=DhbE DhbE]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 59 kDa, 5.684~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1617 bp, 539 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[dhbB]]'', ''[[dhbC]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU31980 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU31980 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU31980 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:dhbE_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=dhbE_3288641_3290260_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:dhbE_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU31980]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[acquisition of iron]]}},~~
−	~~{{SubtiWiki category\|[[iron metabolism]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Fur regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU31980
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU31980&redirect=T BSU31980]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dhbACEBF.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11020]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' ATP-dependent AMP-binding enzyme family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU31980&redirect=T BSU31980]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MDB 1MDB] (complex with DHB-adenylate), [http://www.rcsb.org/pdb/explore.do?structureId=1MDF 1MDF]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P40871 P40871]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31980]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[dhbA]]-[[dhbC]]-[[dhbE]]-[[dhbB]]-[[dhbF]]'' {{PubMed\|8921902}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dhbE_3288641_3290260_-1 dhbE] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|8550523}}
−
−	* '''Regulation:'''
−	** induced by iron starvation ([[Fur]]) {{PubMed\|12354229}}
−
−	* '''Regulatory mechanism:'''
−	** [[Fur]]: transcription repression {{PubMed\|12354229}}
−	** [[AbrB]]: transcription repression {{PubMed\|20817675}}
−
−	* '''Additional information:'''
−	** the amount of the mRNA is substantially decreased upon depletion of [[Rny\|RNase Y]] {{PubMed\|21815947}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 4899 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 1656 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 10561 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 4162 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3499 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>12221282,11112781,11790741,12354229, 8921902 8550523 20817675 21815947</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 126: / Line 126: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 4899 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 1656 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 124: / Line 124: @@
 * '''Additional information:'''
 ** the amount of the mRNA is substantially decreased upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}
 =Biological materials =

@@ 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=BSU31980 dhbE]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 59 kDa, 5.684

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dhbACEBF.html]
@@ Line 92: / Line 93: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MDB 1MDB] (complex with DHB-adenylate),  [http://www.rcsb.org/pdb/explore.do?structureId=1MDF 1MDF]

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 113: / Line 109: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dhbE_3288641_3290260_-1 dhbE] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|8550523}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8550523}}
 * '''Regulation:'''
@@ Line 146: / Line 142: @@
 =References=
-'''Additional publications:''' {{PubMed|20817675}}
+<pubmed>12221282,11112781,11790741,12354229, 8921902 8550523 20817675 21815947</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=dhbE_3288641_3290260_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:dhbE_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dhbE_3288641_3290260_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:dhbE_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU31980]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dhbB]]'', ''[[dhbC]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU31980 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU31980 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU31980 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU31980 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU31980 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU31980 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:dhbE_context.gif]]

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of the siderophore bacillibactin
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 59 kDa, 5.684