Vpr - Revision history

Jstuelk: /* This gene is a member of the following regulons */

2015-06-01T10:17:19Z

‎This gene is a member of the following regulons

Jstuelk at 09:33, 1 June 2015

2015-06-01T09:33:15Z

Jstuelk: /* This gene is a member of the following regulons */

2015-02-11T12:32:48Z

‎This gene is a member of the following regulons

Jstuelk: /* Expression and regulation */

2015-02-11T12:32:20Z

‎Expression and regulation

Jstuelk at 12:26, 11 February 2015

2015-02-11T12:26:59Z

134.76.70.252 at 14:16, 17 April 2014

2014-04-17T14:16:26Z

134.76.38.147 at 15:07, 2 April 2014

2014-04-02T15:07:22Z

Jstuelk at 16:55, 20 February 2014

2014-02-20T16:55:07Z

134.76.70.252 at 14:52, 16 May 2013

2013-05-16T14:52:56Z

134.76.70.252 at 11:35, 14 May 2013

2013-05-14T11:35:25Z

← Older revision		Revision as of 10:17, 1 June 2015
Line 1:		Line 1:
−	* '''Description:~~''' minor extracellular serine protease <br/><br/>~~	+	{{#bank: Vpr}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''vpr''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ipa-45r ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| minor extracellular serine protease~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| protein degradation~~
−	\|-
−	\|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=BSU38090 vpr]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 85 kDa, 5.773~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2418 bp, 806 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ywcI]]'', ''[[ywcH]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU38090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU38090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU38090 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:vpr_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=vpr_3907844_3910264_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:vpr_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38090]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[utilization of nitrogen sources other than amino acids]]}},~~
−	~~{{SubtiWiki category\|[[proteolysis]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[DnaAregulon]]}},~~
−	~~{{SubtiWiki regulon\|[[LexA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[PhoP regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigH regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU38090
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU38090&redirect=T BSU38090]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/vpr.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10591]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' peptidase S8 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU38090&redirect=T BSU38090]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P29141 P29141]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU38090]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''vpr'' {{PubMed\|9353933}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=vpr_3907844_3910264_1 vpr] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigH]] {{PubMed\|25666135}}
−
−	* '''Regulation:'''
−	** expressed under conditions of phosphate limitation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16291680 PubMed]
−	** repressed when no DNA damage is present ([[LexA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
−	** repressed during growth in the presence of branched chain amino acids ([[CodY]]) {{PubMed\|25666135}}
−
−	* '''Regulatory mechanism:'''
−	** [[CodY]]: transcription repression {{PubMed\|25666135}}
−	** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/16291680 PubMed]
−	** [[LexA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
−	** [[DnaA]]: transcription repression {{PubMed\|26020636}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 248 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 175 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 224 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>20735481 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>2106512, 24115457,16291680,16267290,18957862, 25666135 26020636</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 43: / Line 43: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[CodY regulon]]}},
 {{SubtiWiki regulon|[[LexA regulon]]}},
 {{SubtiWiki regulon|[[PhoP regulon]]}},
@@ Line 121: / Line 122: @@
 ** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/16291680 PubMed]
 ** [[LexA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
 * '''Additional information:'''
@@ Line 148: / Line 150: @@
 <pubmed>20735481 </pubmed>
 ==Original publications==
-<pubmed>2106512, 24115457,16291680,16267290,18957862, 25666135</pubmed>
+<pubmed>2106512, 24115457,16291680,16267290,18957862, 25666135 26020636</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 44: / Line 44: @@
 {{SubtiWiki regulon|[[CodY regulon]]}},
 {{SubtiWiki regulon|[[LexA regulon]]}},
-{{SubtiWiki regulon|[[PhoP regulon]]}}
+{{SubtiWiki regulon|[[PhoP regulon]]}},
 =The gene=

@@ Line 109: / Line 109: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=vpr_3907844_3910264_1 vpr] {{PubMed|22383849}}
-* '''[[Sigma factor]]:'''
+* '''[[Sigma factor]]:''' [[SigH]] {{PubMed|25666135}}
 * '''Regulation:'''

@@ Line 42: / Line 42: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[LexA regulon]]}},
 {{SubtiWiki regulon|[[PhoP regulon]]}}
@@ Line 113: / Line 114: @@
 ** expressed under conditions of phosphate limitation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16291680 PubMed]
 ** repressed when no DNA damage is present ([[LexA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
 * '''Regulatory mechanism:'''
 ** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/16291680 PubMed]
 ** [[LexA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16267290 PubMed]
@@ Line 144: / Line 147: @@
 <pubmed>20735481 </pubmed>
 ==Original publications==
-<pubmed>2106512, 24115457,16291680,16267290,18957862, </pubmed>
+<pubmed>2106512, 24115457,16291680,16267290,18957862, 25666135</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 119: / Line 119: @@
 * '''Additional information:'''
 =Biological materials =
 * '''Mutant:'''

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/vpr.html]
@@ Line 89: / Line 90: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 60: / Line 60: @@
 === Additional information===
 =The protein=
@@ Line 78: / Line 75: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 109: / Line 106: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=vpr_3907844_3910264_1 vpr] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 143: / Line 140: @@
 <pubmed>20735481 </pubmed>
 ==Original publications==
-<pubmed>2106512,,16291680,16267290,18957862, </pubmed>
+<pubmed>2106512, 24115457,16291680,16267290,18957862, </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=vpr_3907844_3910264_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:vpr_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=vpr_3907844_3910264_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:vpr_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU38090]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywcI]]'', ''[[ywcH]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU38090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU38090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU38090 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU38090 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU38090 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU38090 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:vpr_context.gif]]