ClpE - Revision history

Jstuelk: /* Biological materials */

2015-06-16T10:57:41Z

‎Biological materials

134.76.70.252 at 09:39, 17 April 2014

2014-04-17T09:39:59Z

134.76.38.147 at 13:33, 2 April 2014

2014-04-02T13:33:10Z

134.76.70.252 at 10:38, 7 January 2014

2014-01-07T10:38:06Z

134.76.70.252 at 16:07, 11 November 2013

2013-11-11T16:07:12Z

134.76.70.252 at 13:07, 16 May 2013

2013-05-16T13:07:11Z

134.76.70.252 at 10:03, 14 May 2013

2013-05-14T10:03:08Z

134.76.70.252 at 12:40, 13 May 2013

2013-05-13T12:40:24Z

Jstuelk at 11:35, 14 March 2013

2013-03-14T11:35:52Z

Jstuelk at 11:35, 14 March 2013

2013-03-14T11:35:34Z

← Older revision		Revision as of 10:57, 16 June 2015
Line 1:		Line 1:
−	* '''Description:~~''' ATP-dependent Clp protease-like (class III stress gene) <br/><br/>~~	+	{{#bank: ClpE}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''clpE''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ykvH ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| ATP-dependent Clp protease-like~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| protein 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=BSU13700 clpE]
−	\|-
−	\|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=ClpE ClpE]
−	\|-
−	\|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=clpE clpE]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 77 kDa, 5.135~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2097 bp, 699 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[motA]]'', ''[[ykvI]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13700 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13700 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13700 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:clpE_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=clpE_1435628_1437727_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:clpE_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13700]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[proteolysis]]}},~~
−	~~{{SubtiWiki category\|[[heat shock proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CtsR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU13700
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13700&redirect=T BSU13700]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpE.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12578]
−
−	~~=== Additional information===~~
−	* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed\|21821766}}
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
−
−	* '''Protein family:''' AAA+ -type ATPase (IPR013093) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR013093 InterPro] (PF07724) [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
−
−	* '''Paralogous protein(s):''' [[ClpC]], [[ClpX]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:''' AAA-ATPase [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[ClpE]]-[[ClpP]]
−
−	* '''[[Localization]]:'''
−	** localization in cytoplasmic polar clusters, excluded from the nucleoid, colocalization with [[ClpP]] [http://www.ncbi.nlm.nih.gov/pubmed/18786145 Pubmed]
−	** forms foci coincident with nucleoid edges, usually near cell poles {{PubMed\|18689473}}
−	~~[[File:ClpE.jpg‎ ]]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13700&redirect=T BSU13700]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O31673 O31673]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13700]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''clpE'' {{PubMed\|10320580}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=clpE_1435628_1437727_-1 clpE] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|10320580}}
−
−	* '''Regulation:'''
−	** induced by heat ([[CtsR]]) {{PubMed\|10320580,9987115}}
−
−	* '''Regulatory mechanism:'''
−	** [[CtsR]]: transcription repression {{PubMed\|10320580,9987115,11179229,16163393,17380125}}
−
−	* '''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): 420 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' ''clpE::spec'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:''' C-terminal YFP and CFP fusions (single copy) available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	~~[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~'''Additional reviews:''' {{PubMed\|23479438}}~~
−	~~<pubmed> 17302811 </pubmed>~~
−	~~==Original Publications==~~
−	~~'''Additional publications:''' {{PubMed\|16163393,17380125}}~~
−	~~<pubmed>10320580 9987115 11179229 21821766</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:39, 17 April 2014
Line 125:		Line 125:

	* '''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): 420 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpE.html]
@@ Line 97: / Line 98: @@
 === 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=ClpE ClpE]
 |-
-|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/stress_response.html Stress]'''
+|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=clpE clpE]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 77 kDa, 5.135

@@ 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=BSU13700 clpE]
 |-
-|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/ClpE ClpE]
+|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=ClpE ClpE]
 |-
 |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/stress_response.html Stress]'''

@@ 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=clpE_1435628_1437727_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:clpE_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=clpE_1435628_1437727_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:clpE_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13700]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[motA]]'', ''[[ykvI]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13700 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13700 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13700 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13700 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13700 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13700 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:clpE_context.gif]]

@@ Line 145: / Line 145: @@
 =References=
 ==Reviews==
-'''Additional reviews:''' {{PubMed|23479438,19609260,19781636}}
+'''Additional reviews:''' {{PubMed|23479438}}
 <pubmed> 17302811 </pubmed>
 ==Original Publications==

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 118: / Line 114: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=clpE_1435628_1437727_-1 clpE] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|10320580}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|10320580}}
 * '''Regulation:'''
@@ Line 149: / Line 145: @@
 =References=
 ==Reviews==
 <pubmed> 17302811 </pubmed>
 ==Original Publications==