SinI - Revision history

Jstuelk: /* Biological materials */

2015-07-21T08:08:32Z

‎Biological materials

134.76.38.147 at 14:12, 2 April 2014

2014-04-02T14:12:09Z

134.76.70.252 at 11:12, 7 January 2014

2014-01-07T11:12:04Z

Jstuelk: /* Original publications */

2013-11-29T17:59:22Z

‎Original publications

134.76.70.252 at 08:50, 12 November 2013

2013-11-12T08:50:32Z

Czschiedrich: /* Biological materials */

2013-11-01T13:26:32Z

‎Biological materials

134.76.70.252 at 13:54, 16 May 2013

2013-05-16T13:54:05Z

134.76.70.252 at 10:42, 14 May 2013

2013-05-14T10:42:34Z

134.76.70.252 at 13:17, 13 May 2013

2013-05-13T13:17:05Z

Jstuelk: /* Original publications */

2013-03-27T11:50:02Z

‎Original publications

← Older revision		Revision as of 08:08, 21 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' antagonist of [[SinR]], drives [[SlrR]] from the [[SlrR]](LOW) to the [[SlrR]](HIGH) state <br/><br/>~~	+	{{#bank: SinI}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''sinI''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| antagonist of [[SinR]]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of [[biofilm formation]]~~
−	\|-
−	\|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=BSU24600 sinI]
−	\|-
−	\|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=SinI SinI]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=sinI sinI]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 6 kDa, 6.333~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 171 bp, 57 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yqhG]]'', ''[[sinR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24600 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:sinI_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=sinI_2552446_2552619_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:sinI_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24600]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[transition state regulators]]}},~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[ScoC regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU24600
−
−	~~===Phenotypes of a mutant ===~~
−	* altered cell death pattern in colonies {{PubMed\|23012477}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24600&redirect=T BSU24600]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sinIR.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10753]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[SlrA]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[SinR]]-[[SinI]] {{PubMed\|9799632}}, K(D) 1.8 nM {{PubMed\|23430750}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU24600&redirect=T BSU24600]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0N 1B0N] (complex [[SinR]]-[[SinI]]) {{PubMed\|9799632}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P23308 P23308]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24600]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[sinI]]-[[sinR]]'' {{PubMed\|3125149}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sinI_2552446_2552619_1 sinI] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|3125149}}
−
−	* '''Regulation:'''
−	** activated under conditions that trigger sporulation by ([[Spo0A]]) interaction [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed],{{PubMed\|21326214}}
−	** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
−	** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
−	** repressed during vegetative growth ([[SinR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[Spo0A]]: transcription activation, in a portion of cells [http://www.ncbi.nlm.nih.gov/sites/entrez/11751836 PubMed]
−	** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1906467,11751836 PubMed]
−	** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7635837,11751836 PubMed]
−	** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1664536 PubMed]
−
−	* '''Additional information:'''
−	** the mRNA is substantially stabilized upon depletion of [[Rny\|RNase Y]] {{PubMed\|21815947}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP959 (spc), available in [[Stülke]] lab
−	** DS91 (spc) NCIB3610 derivate, available in [[Stülke]] lab
−	** 1S98 ( ''sinI''::''kan''), {{PubMed\|11466285}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S98&Search=1S98 BGSC]
−	** GP1663 (''yghG-sinI-sinR-tasA''), available in [[Stülke]] lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
−
−	* '''FLAG-tag construct (C-term):''' GP935 (kan), available in [[Stülke]] lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/ protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 20541494 </pubmed>~~
−	~~==Modelling of the [[SinI]]/[[SinR]] switch==~~
−	~~<pubmed> 21095906 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>23430750 23012477,21326214 21815947 3125149 15661000,18047568,,11751836,1906467,11751836,7635837,11751836, 10547280, 15104138, 9799632 20923420 8422983 24256735 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 61: / Line 61: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sinIR.html]
@@ Line 99: / Line 100: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1B0N 1B0N] (complex [[SinR]]-[[SinI]]) {{PubMed|9799632}}

@@ 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=SinI SinI]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=sinI sinI]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 6.333

@@ Line 163: / Line 163: @@
 <pubmed> 21095906 </pubmed>
 ==Original publications==
-<pubmed>23430750 23012477,21326214 21815947 3125149  15661000,18047568,,11751836,1906467,11751836,7635837,11751836, 10547280, 15104138, 9799632 20923420 8422983 </pubmed>
+<pubmed>23430750 23012477,21326214 21815947 3125149  15661000,18047568,,11751836,1906467,11751836,7635837,11751836, 10547280, 15104138, 9799632 20923420 8422983 24256735 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=BSU24600 sinI]
 |-
-|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/SinI SinI]
+|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=SinI SinI]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm]'''

@@ Line 139: / Line 139: @@
 ** DS91 (spc) NCIB3610 derivate, available in [[Stülke]] lab
 ** 1S98 ( ''sinI''::''kan''), {{PubMed|11466285}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S98&Search=1S98 BGSC]
 * '''Expression vector:'''

@@ 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=sinI_2552446_2552619_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sinI_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sinI_2552446_2552619_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sinI_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24600]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqhG]]'', ''[[sinR]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24600 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24600 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:sinI_context.gif]]