IspF - Revision history

134.76.70.252 at 11:43, 8 April 2014

2014-04-08T11:43:14Z

134.76.38.147 at 12:48, 2 April 2014

2014-04-02T12:48:22Z

Jstuelk at 15:55, 12 July 2013

2013-07-12T15:55:32Z

Jstuelk at 11:49, 11 July 2013

2013-07-11T11:49:42Z

Jstuelk at 08:09, 9 July 2013

2013-07-09T08:09:50Z

134.76.70.252 at 12:21, 16 May 2013

2013-05-16T12:21:13Z

134.76.70.252 at 09:14, 14 May 2013

2013-05-14T09:14:36Z

134.76.70.252 at 11:57, 13 May 2013

2013-05-13T11:57:28Z

134.76.70.252 at 13:08, 8 August 2012

2012-08-08T13:08:41Z

134.76.70.252 at 08:57, 8 August 2012

2012-08-08T08:57:38Z

← Older revision		Revision as of 11:43, 8 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' 2-C-methyl-D-erythrol-2,4-cyclodiphosphate synthase, 5th step in the MEP pathway of isoprenoid biosynthesis <br/><br/>~~	+	{{#bank: IspF}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ispF''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yacN''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| 2-C-methyl-D-erythrol-2,4-cyclodiphosphate synthase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| MEP pathway of isoprenoid biosynthesis~~
−	\|-
−	\|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=BSU00910 ispF]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 16 kDa, 5.398~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 474 bp, 158 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ispD]]'', ''[[gltX]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00910 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yacN_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=ispF_110480_110956_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ispF_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00910]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biosynthesis of lipids]]}},~~
−	~~{{SubtiWiki category\|[[general stress proteins (controlled by SigB)]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigB regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00910
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00910&redirect=T BSU00910]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yacLMN.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10153]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + CMP (according to Swiss-Prot)
−
−	* '''Protein family:''' ispF 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]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00910&redirect=T BSU00910]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1T0A 1T0A] (from ''Shewanella oneidensis'', 62% identity) {{PubMed\|15502301}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/Q06756 Q06756]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00910]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/4.6.1.12 4.6.1.12]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[yacL]]-[[ispD]]-[[ispF]]'' {{PubMed\|10482513}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ispF_110480_110956_1 ispF] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
−	* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>15805528, 10482513 12270818 17458547 23840410 15502301 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yacLMN.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:'''	[http://www.rcsb.org/pdb/explore/explore.do?structureId=1T0A 1T0A] (from ''Shewanella oneidensis'', 62% identity) {{PubMed|15502301}}

@@ Line 94: / Line 94: @@
 === Database entries ===
-* '''Structure:'''
+* '''Structure:'''	[http://www.rcsb.org/pdb/explore/explore.do?structureId=1T0A 1T0A] (from ''Shewanella oneidensis'', 62% identity) {{PubMed|15502301}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/Q06756 Q06756]
@@ Line 138: / Line 138: @@
 =References=
-<pubmed>15805528, 10482513 12270818 17458547 23840410 </pubmed>
+<pubmed>15805528, 10482513 12270818 17458547 23840410 15502301 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 138: / Line 138: @@
 =References=
-<pubmed>15805528, 10482513 12270818 17458547 </pubmed>
+<pubmed>15805528, 10482513 12270818 17458547 23840410 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 1: / Line 1: @@
-* '''Description:''' 2-C-methyl-D-erythrol-2,4-cyclodiphosphate synthase <br/><br/>
+* '''Description:''' 2-C-methyl-D-erythrol-2,4-cyclodiphosphate synthase, 5th step in the MEP pathway of isoprenoid biosynthesis <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || 2-C-methyl-D-erythrol-2,4-cyclodiphosphate synthase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || isoprenoid biosynthesis
+|style="background:#ABCDEF;" align="center"|'''Function''' || MEP pathway of isoprenoid biosynthesis
 |-
 |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=BSU00910 ispF]
@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 114: / Line 110: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ispF_110480_110956_1 ispF] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
+* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 * '''Regulation:'''  induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]

@@ 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=ispF_110480_110956_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ispF_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ispF_110480_110956_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ispF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00910]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ispD]]'', ''[[gltX]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00910 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00910 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yacN_context.gif]]

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || isoprenoid biosynthesis
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.398