YvyD - Revision history

Jstuelk at 10:26, 11 June 2015

2015-06-11T10:26:13Z

Jstuelk at 13:06, 11 February 2015

2015-02-11T13:06:46Z

Jstuelk: /* Expression and regulation */

2015-02-11T13:05:15Z

‎Expression and regulation

Jstuelk: /* Expression and regulation */

2015-02-11T13:05:03Z

‎Expression and regulation

134.76.70.252 at 09:31, 17 April 2014

2014-04-17T09:31:12Z

134.76.38.147 at 14:55, 2 April 2014

2014-04-02T14:55:26Z

Jstuelk: /* References */

2014-03-27T16:48:50Z

‎References

Jstuelk at 19:32, 15 September 2013

2013-09-15T19:32:16Z

134.76.70.252 at 14:42, 16 May 2013

2013-05-16T14:42:00Z

134.76.70.252 at 11:24, 14 May 2013

2013-05-14T11:24:02Z

← Older revision		Revision as of 10:26, 11 June 2015
Line 1:		Line 1:
−	* '''Description:~~''' general stress protein, required for ribosome dimerization in the stationary phase, required for protection against paraquat stress <br/><br/>~~	+	{{#bank: YvyD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yvyD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yviI ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| unknown~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| dimerization of ribosomes in the stationary phase, protection against paraquat stress~~
−	\|-
−	\|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=BSU35310 yvyD]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 21 kDa, 5.184~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 567 bp, 189 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[secA]]'', ''[[smiA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35310 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35310 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35310 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yvyD_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=yvyD_3631003_3631572_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yvyD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35310]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[general stress proteins (controlled by SigB)]]}},~~
−	~~{{SubtiWiki category\|[[resistance against oxidative and electrophile stress]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[PhoP regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigH regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU35310
−
−	~~===Phenotypes of a mutant ===~~
−	* the mutant is cold-sensitive
−	* delayed recovery from stationary phase and delayed [[germination]]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35310&redirect=T BSU35310]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yvyD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10740]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' ribosomal protein S30Ae family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−	** phosphorylated on Arg-6 {{PubMed\|22517742}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[YvyD]]-[[ribosome]] (for ribosome dimerization) {{PubMed\|22950019}}
−	* '''[[Localization]]:'''
−	** membrane protein
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35310&redirect=T BSU35310]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P28368 P28368]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35310]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''yvyD'' {{PubMed\|9852014}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvyD_3631003_3631572_-1 yvyD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigB]] {{PubMed\|9852014,15805528}}, [[SigH]] {{PubMed\|9852014}}
−
−	* '''Regulation:'''
−	** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−	** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−	** induced under conditions of phosphate limitation ([[PhoP]]) {{PubMed\|25666134}}
−
−	* '''Regulatory mechanism:'''
−	** [[PhoP]]: transcription activation {{PubMed\|25666134}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2138 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3361 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>11948165,9852014,10913081,22517742,12107147 15805528 22950019 22582280 25666134</pubmed>~~
−	~~==Publications on the homologous proteins from other bacteria==~~
−	~~<pubmed> 22605777 24279750 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 44: / Line 44: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[SigB regulon]]}},
 {{SubtiWiki regulon|[[SigH regulon]]}}
@@ Line 147: / Line 148: @@
 =References=
-<pubmed>11948165,9852014,10913081,22517742,12107147 15805528 22950019 22582280</pubmed>
+<pubmed>11948165,9852014,10913081,22517742,12107147 15805528 22950019 22582280 25666134</pubmed>
 ==Publications on the homologous proteins from other bacteria==
 <pubmed> 22605777 24279750 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 123: / Line 123: @@
 * '''Regulatory mechanism:'''
 ** [[PhoP]]: transcription activation {{PubMed|25666134}}
 * '''Additional information:'''

@@ Line 119: / Line 119: @@
 ** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
 ** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 * '''Regulatory mechanism:'''
 * '''Additional information:'''

← Older revision		Revision as of 09:31, 17 April 2014
Line 123:		Line 123:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2138 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3361 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yvyD.html]
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 1: / Line 1: @@
-* '''Description:''' general stress protein, required for ribosome dimerization in the stationary phase<br/><br/>
+* '''Description:''' general stress protein, required for ribosome dimerization in the stationary phase, required for protection against paraquat stress <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || dimerization of ribosomes in the stationary phase
+|style="background:#ABCDEF;" align="center"|'''Function''' || dimerization of ribosomes in the stationary phase, protection against paraquat stress
 |-
 |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=BSU35310 yvyD]
@@ Line 39: / Line 39: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},
 {{SubtiWiki category|[[membrane proteins]]}},
 {{SubtiWiki category|[[phosphoproteins]]}}
@@ Line 111: / Line 112: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvyD_3631003_3631572_-1 yvyD] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigB]] {{PubMed|9852014,15805528}}, [[SigH]] {{PubMed|9852014}}
+* '''[[Sigma factor]]:''' [[SigB]] {{PubMed|9852014,15805528}}, [[SigH]] {{PubMed|9852014}}
 * '''Regulation:'''
@@ Line 140: / Line 141: @@
 =References=
-'''Additional publications:''' {{PubMed|22950019}}
+<pubmed>11948165,9852014,10913081,22517742,12107147 15805528 22950019 22582280</pubmed>
 ==Publications on the homologous ''E. coli'' proteins Hpf and YfiA==
 <pubmed> 22605777 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=yvyD_3631003_3631572_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yvyD_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yvyD_3631003_3631572_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yvyD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35310]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[secA]]'', ''[[smiA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35310 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35310 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35310 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35310 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35310 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35310 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yvyD_context.gif]]