SipW - Revision history

134.76.38.147 at 14:12, 2 April 2014

2014-04-02T14:12:26Z

134.76.70.252 at 11:12, 7 January 2014

2014-01-07T11:12:18Z

134.76.70.252 at 08:50, 12 November 2013

2013-11-12T08:50:52Z

Jstuelk at 13:40, 31 July 2013

2013-07-31T13:40:47Z

Jstuelk at 15:18, 24 May 2013

2013-05-24T15:18:35Z

134.76.70.252 at 13:54, 16 May 2013

2013-05-16T13:54:22Z

134.76.70.252 at 10:42, 14 May 2013

2013-05-14T10:42:52Z

134.76.70.252 at 13:17, 13 May 2013

2013-05-13T13:17:26Z

134.76.70.252 at 12:13, 19 September 2012

2012-09-19T12:13:58Z

134.76.70.252 at 11:38, 7 August 2012

2012-08-07T11:38:08Z

← Older revision		Revision as of 14:12, 2 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' bifunctional signal peptidase I that controls surface-adhered [[biofilm formation]] and processes [[TasA]] and [[TapA]]<br/><br/>~~	+	{{#bank: SipW}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''sipW''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yqhE ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| signal peptidase I~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[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=BSU24630 sipW]
−	\|-
−	\|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=SipW SipW]
−	\|-
−	\|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=sipW sipW]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 20 kDa, 5.494~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 570 bp, 190 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[tasA]]'', ''[[tapA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24630 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24630 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24630 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:sipW_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=sipW_2553930_2554502_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:sipW_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24630]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[protein secretion]]}},~~
−	~~{{SubtiWiki category\|[[biofilm formation]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[RemA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SinR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU24630
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yqxM-sipW-tasA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11696]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** important for [[biofilm formation]] on a solid surface, but not required at an air-liquid interface {{PubMed\|22328672}}
−	** Cleavage of hydrophobic, N-terminal signal or leader sequences from [[TasA]] and [[TapA]] {{PubMed\|10049401,10559173}}
−
−	* '''Protein family:''' peptidase S26B 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]]:'''
−	** [[SipW]]-[[TapA]] {{PubMed\|10559173}}
−	** [[SipW]]-[[TasA]] {{PubMed\|10049401}}
−
−	* '''[[Localization]]:'''
−	** membrane {{PubMed\|22328672}}
−
−	~~=== Database entries ===~~
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P54506 P54506]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU24630]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[tapA]]-[[sipW]]-[[tasA]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sipW_2553930_2554502_-1 sipW] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
−
−	* '''Regulation:'''
−	** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
−	** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10464223,17720793 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10464223,17720793 PubMed]
−	** [[SinR]]: transcription repression {{PubMed\|16430695}}
−	** [[RemA]]: transcription activation {{PubMed\|23646920}}
−
−	* '''Additional information:'''
−	** induction by sequestration of [[SinR]] by [[SinI]] or [[SlrA]] {{PubMed\|15661000,19788541}} or by [[SlrR]] {{PubMed\|20351052}}
−	** the ''[[tapA]]-[[sipW]]-[[tasA]]'' operon is not expressed in a ''[[ymdB]]'' mutant {{PubMed\|21856853}}
−	** the amount of the mRNA is substantially decreased upon depletion of [[Rny\|RNase Y]] (this is likely due to the increased stability of the ''[[sinR]]'' mRNA) {{PubMed\|21815947}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A937 ( ''sipW''::''kan''), {{PubMed\|15101989}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A937&Search=1A937 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	* [[Beth Lazazzera]], Los Angeles, USA
−
−	~~=Your additional remarks=~~
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>21488983 22427624 22688815 </pubmed>~~
−	~~== Original publications ==~~
−	~~<pubmed> 22328672 18047568,15175311,16430695,10368135,9694797,18430133,18647168,10464223,17720793, 20351052 10827084 21477127 10559173 23646920 21856853 21815947</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ 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=SipW SipW]
 |-
-|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], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
+|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=sipW sipW]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 5.494

@@ 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=BSU24630 sipW]
 |-
-|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/SipW SipW]
+|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=SipW SipW]
 |-
 |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], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''

@@ Line 154: / Line 154: @@
 =References=
 ==Reviews==
-<pubmed>21488983 22427624</pubmed>
+<pubmed>21488983 22427624 22688815 </pubmed>
 == Original publications ==
 <pubmed> 22328672 18047568,15175311,16430695,10368135,9694797,18430133,18647168,10464223,17720793, 20351052 10827084 21477127 10559173 23646920 21856853 21815947</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 52: / Line 48: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[AbrB regulon]]}},
 {{SubtiWiki regulon|[[SinR regulon]]}}
@@ Line 120: / Line 117: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sipW_2553930_2554502_-1 sipW] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
+* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16430695 PubMed]
 * '''Regulation:'''
@@ Line 129: / Line 126: @@
 ** [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10464223,17720793 PubMed]
 ** [[SinR]]: transcription repression {{PubMed|16430695}}
 * '''Additional information:'''
@@ Line 156: / Line 154: @@
 =References=
 ==Reviews==
-'''Additional reviews:''' {{PubMed|22427624}}
+<pubmed>21488983 22427624</pubmed>
 ==Original publications==
-<pubmed> 22328672</pubmed>
+<pubmed> 22328672 18047568,15175311,16430695,10368135,9694797,18430133,18647168,10464223,17720793, 20351052 10827084 21477127 10559173 23646920 21856853 21815947</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=sipW_2553930_2554502_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sipW_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sipW_2553930_2554502_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:sipW_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU24630]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tasA]]'', ''[[tapA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24630 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24630 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24630 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU24630 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU24630 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU24630 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:sipW_context.gif]]

← Older revision		Revision as of 12:13, 19 September 2012
Line 138:		Line 138:

	* '''Mutant:'''		* '''Mutant:'''
		+	** 1A937 ( ''sipW''::''kan''), {{PubMed\|15101989}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A937&Search=1A937 BGSC]

	* '''Expression vector:'''		* '''Expression vector:'''

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || [[biofilm formation]]
 |-
 |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/SipW SipW]