SpsK - Revision history

Jstuelk at 07:49, 19 August 2015

2015-08-19T07:49:13Z

Jstuelk: /* Expression and regulation */

2015-04-06T14:12:10Z

‎Expression and regulation

Jstuelk at 11:36, 23 September 2014

2014-09-23T11:36:05Z

134.76.38.147 at 15:06, 2 April 2014

2014-04-02T15:06:31Z

134.76.70.252 at 14:51, 16 May 2013

2013-05-16T14:51:59Z

134.76.70.252 at 11:34, 14 May 2013

2013-05-14T11:34:28Z

134.76.70.252 at 14:08, 13 May 2013

2013-05-13T14:08:49Z

Jstuelk at 16:10, 18 September 2012

2012-09-18T16:10:42Z

134.76.70.252 at 17:08, 7 August 2012

2012-08-07T17:08:29Z

134.76.70.252 at 11:37, 23 April 2012

2012-04-23T11:37:29Z

← Older revision		Revision as of 07:49, 19 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' dTDP -4-dehydrorhamnose reductase, spore coat polysaccharide synthesis <br/><br/>~~	+	{{#bank: SpsK}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''spsK''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ipa-73d ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| dTDP -4-dehydrorhamnose reductase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| rhamnose biosynthesis, spore coat polysaccharide synthesis~~
−	\|-
−	\|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=BSU37820 spsK]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 31 kDa, 6.081~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 849 bp, 283 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[spsL]]'', ''[[spsJ]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37820 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37820 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37820 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:spsK_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=spsK_3883427_3884278_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:spsK_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU37820]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[miscellaneous metabolic pathways]]}},~~
−	~~{{SubtiWiki category\|[[sporulation proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[GerE regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigK regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU37820
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU37820&redirect=T BSU37820]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sps.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10619]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' dTDP-4-dehydrorhamnose reductase 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=BSU37820&redirect=T BSU37820]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3SC6 3SC6] (dTDP-4-dehydrorhamnose reductase (''rfbD'') from ''Bacillus anthracis'' str. Ames in complex with NADP; 42% identity, 72% similarity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P39631 P39631]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37820]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.133 1.1.1.133]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[spsA]]-[[spsB]]-[[spsC]]-[[spsD]]-[[spsE]]-[[spsF]]-[[spsG]]-[[spsI]]-[[spsJ]]-[[spsK]]-[[spsL]]'' {{PubMed\|9353933}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spsK_3883427_3884278_-1 spsK] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigK]] {{PubMed\|15383836}}
−
−	* '''Regulation:'''
−	** expressed late during sporulation in the mother cell ([[SigK]], [[GerE]]) {{PubMed\|25239894,15383836}}
−
−	* '''Regulatory mechanism:'''
−	** [[GerE]]: transcription activation {{PubMed\|25239894,15383836}}
−
−	* '''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>9353933 15383836 22960854 25239894</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 104: / Line 104: @@
 =Expression and regulation=
-* '''Operon:''' ''[[spsA]]-[[spsB]]-[[spsC]]-[[spsD]]-[[spsF]]-[[spsG]]-[[spsI]]-[[spsJ]]-[[spsK]]-[[spsL]]'' {{PubMed|9353933}}
+* '''Operon:''' ''[[spsA]]-[[spsB]]-[[spsC]]-[[spsD]]-[[spsE]]-[[spsF]]-[[spsG]]-[[spsI]]-[[spsJ]]-[[spsK]]-[[spsL]]'' {{PubMed|9353933}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spsK_3883427_3884278_-1 spsK] {{PubMed|22383849}}

@@ Line 44: / Line 44: @@
 = This gene is a member of the following [[regulons]] =
-{{SubtiWiki regulon|[[SigE regulon]]}},
+{{SubtiWiki regulon|[[GerE regulon]]}},
 {{SubtiWiki regulon|[[SigK regulon]]}}
@@ Line 63: / Line 63: @@
 === Additional information===
 =The protein=
@@ Line 111: / Line 108: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spsK_3883427_3884278_-1 spsK] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigK]] {{PubMed|15383836}}
+* '''[[Sigma factor]]:''' [[SigK]] {{PubMed|15383836}}
 * '''Regulation:'''
-** expressed late during sporulation in the mother cell ([[SigK]]) {{PubMed|15383836}}
+** expressed late during sporulation in the mother cell ([[SigK]], [[GerE]]) {{PubMed|25239894,15383836}}
 * '''Regulatory mechanism:'''
 * '''Additional information:'''
@@ Line 139: / Line 137: @@
 =References=
-<pubmed>9353933 15383836 22960854 </pubmed>
+<pubmed>9353933 15383836 22960854 25239894</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sps.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3SC6 3SC6] (dTDP-4-dehydrorhamnose reductase (''rfbD'') from ''Bacillus anthracis'' str. Ames in complex with NADP; 42% identity, 72% similarity)

@@ 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=spsK_3883427_3884278_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:spsK_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spsK_3883427_3884278_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:spsK_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU37820]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spsL]]'', ''[[spsJ]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37820 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37820 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37820 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37820 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37820 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37820 DNA_with_flanks]
 |-
 |-

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || rhamnose biosynthesis, spore coat polysaccharide synthesis
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU37820 spsK]
+|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=BSU37820 spsK]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 6.081
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spsL]]'', ''[[spsJ]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15808&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU37820 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU37820 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU37820 Advanced_DNA]
 |-
 |-

@@ Line 1: / Line 1: @@
-* '''Description:''' spore coat polysaccharide synthesis <br/><br/>
+* '''Description:''' dTDP -4-dehydrorhamnose reductase, spore coat polysaccharide synthesis <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+|style="background:#ABCDEF;" align="center"| '''Product''' || dTDP -4-dehydrorhamnose reductase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || spore coat polysaccharide synthesis
+|style="background:#ABCDEF;" align="center"|'''Function''' || rhamnose biosynthesis, spore coat polysaccharide synthesis
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU37820 spsK]
@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[sporulation proteins]]}}
@@ Line 103: / Line 100: @@
 * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37820]
-* '''E.C. number:'''
+* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.133 1.1.1.133]
 === Additional information===
@@ Line 140: / Line 137: @@
 =References=
-<pubmed>9353933 15383836</pubmed>
+<pubmed>9353933 15383836 22960854 </pubmed>
 [[Category:Protein-coding genes]]