YsbB - Revision history

Jstuelk at 10:49, 12 June 2015

2015-06-12T10:49:23Z

Atkovacs at 14:14, 11 June 2015

2015-06-11T14:14:38Z

Atkovacs at 13:30, 9 June 2015

2015-06-09T13:30:49Z

134.76.38.147 at 14:28, 2 April 2014

2014-04-02T14:28:40Z

Jstuelk: /* References */

2013-07-13T16:34:42Z

‎References

134.76.70.252 at 14:14, 16 May 2013

2013-05-16T14:14:20Z

134.76.70.252 at 10:58, 14 May 2013

2013-05-14T10:58:09Z

134.76.70.252 at 13:33, 13 May 2013

2013-05-13T13:33:19Z

Jstuelk at 17:05, 26 November 2012

2012-11-26T17:05:08Z

134.76.70.252 at 14:46, 7 August 2012

2012-08-07T14:46:08Z

← Older revision		Revision as of 10:49, 12 June 2015
Line 1:		Line 1:
−	* '''Description:~~''' putative peptidoglycan hydrolase, probably involved in cell wall turnover <br/><br/>~~	+	{{#bank: YsbB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ysbB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| unknown~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| unknown~~
−	\|-
−	\|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=BSU28900 ysbB]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 24 kDa, 9.81~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 693 bp, 231 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yscB]]'', ''[[ysbA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28900 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28900 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28900 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ysbB_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=lrgB_2954492_2955187_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ysbB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28900]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[cell wall degradation/ turnover]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU28900
−
−	~~===Phenotypes of a mutant ===~~
−	** ''ysbAB'' mutant is delayed in pellicle formation {{PubMed\|26060272}}
−	** ''ywbHG''-''yxaKC''-''ysbAB'' triple mutant is severely delayed in pellicle formation {{PubMed\|26060272}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU28900&redirect=T BSU28900]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ysbB.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12312]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' LrgB subfamily (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=BSU28900&redirect=T BSU28900]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P94516 P94516]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28900]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:'''
−	** ''[[ysbA]]-[[ysbB]]'' {{PubMed\|21815947}}
−	** ''[[ysbB]]'' {{PubMed\|8969504}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lrgB_2954492_2955187_-1 ysbB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** ''ysbAB'' expression is induced by acetate {{PubMed\|26060272}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** the mRNA is substantially stabilized upon depletion of [[Rny\|RNase Y]] {{PubMed\|21815947}}
−	** the expression of the ''[[ysbA]]-[[ysbB]]'' operon is strongly increased in a ''[[cshA]]'' mutant {{PubMed\|23175651}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP1554 (''[[ysbA]]-[[ysbB]]''::''spc''), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed> 26060272 23175651 21815947 8969504 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 52: / Line 52: @@
 ===Phenotypes of a mutant ===
-** ''ysbAB'' mutant is delayed in pellicle formation (Chen et al)
+** ''ysbAB'' mutant is delayed in pellicle formation {{PubMed|26060272}}
-** ''ywbHG''-''yxaKC''-''ysbAB'' triple mutant is severely delayed in pellicle formation (Chen et al)
+** ''ywbHG''-''yxaKC''-''ysbAB'' triple mutant is severely delayed in pellicle formation {{PubMed|26060272}}
 === Database entries ===
@@ Line 116: / Line 116: @@
 * '''Regulation:'''
-** ''ysbAB'' expression is induced by acetate (Chen et al)
+** ''ysbAB'' expression is induced by acetate {{PubMed|26060272}}
 * '''Regulatory mechanism:'''
@@ Line 144: / Line 144: @@
 =References=
-<pubmed> 23175651 21815947 8969504 </pubmed>
+<pubmed> 26060272 23175651 21815947 8969504 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 52: / Line 52: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 114: / Line 116: @@
 * '''Regulation:'''
 * '''Regulatory mechanism:'''

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ysbB.html]
@@ Line 91: / Line 92: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 139: / Line 139: @@
 =References=
-<pubmed> 23175651 </pubmed>
+<pubmed> 23175651 21815947 8969504 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=lrgB_2954492_2955187_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ysbB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lrgB_2954492_2955187_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ysbB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU28900]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yscB]]'', ''[[ysbA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28900 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28900 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28900 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28900 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28900 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28900 DNA_with_flanks]
 |-
 |-

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU28900 ysbB]
+|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=BSU28900 ysbB]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 9.81
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yscB]]'', ''[[ysbA]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14850&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU28900 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU28900 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU28900 Advanced_DNA]
 |-
 |-

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 113: / Line 109: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lrgB_2954492_2955187_-1 ysbB] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 121: / Line 117: @@
 * '''Additional information:'''
 ** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}
 =Biological materials =
@@ Line 142: / Line 139: @@
 =References=
   <big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J''  </big>
   <big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>