PhoP - Revision history

Jstuelk at 16:55, 11 February 2015

2015-02-11T16:55:10Z

Jstuelk at 11:08, 13 June 2014

2014-06-13T11:08:54Z

134.76.70.252 at 09:54, 17 April 2014

2014-04-17T09:54:51Z

134.76.38.147 at 14:29, 2 April 2014

2014-04-02T14:29:36Z

134.76.70.252 at 11:26, 7 January 2014

2014-01-07T11:26:21Z

134.76.70.252 at 09:06, 12 November 2013

2013-11-12T09:06:35Z

134.76.70.252 at 14:15, 16 May 2013

2013-05-16T14:15:25Z

134.76.70.252 at 10:59, 14 May 2013

2013-05-14T10:59:05Z

134.76.70.252 at 13:34, 13 May 2013

2013-05-13T13:34:38Z

134.76.70.252 at 12:30, 19 September 2012

2012-09-19T12:30:14Z

← Older revision		Revision as of 16:55, 11 February 2015
Line 1:		Line 1:
−	* '''Description:~~''' [[two-component systems\|two-component]] response regulator ([[transcription factors of the OmpR family\|OmpR family]]), regulation of phosphate metabolism <br/><br/>~~	+	{{#bank: PhoP}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''phoP''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[two-component systems\|two-component]] response regulator ([[transcription factors of the OmpR family\|OmpR family]])~~
−	\|-
−	\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of [[phosphate metabolism]] <br/>(''[[phoA]], [[phoB]], [[phoD]], [[resA \| resABCDE]], [[tagA]]-[[tagB]], [[tagD \| tagDEF]], [[tuaA \| tuaA-H]]'')
−	\|-
−	\|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=BSU29110 phoP]
−	\|-
−	\|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=PhoP PhoP]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=phoP phoP]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 27 kDa, 5.068~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 720 bp, 240 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[phoR]]'', ''[[mdh]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29110 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:phoP_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=phoP_2977800_2978522_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:phoP_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29110]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[phosphate metabolism]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[regulators of core metabolism]]}},~~
−	~~{{SubtiWiki category\|[[sporulation proteins]]}},~~
−	~~{{SubtiWiki category\|[[general stress proteins (controlled by SigB)]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CcpA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[PhoP regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigE regulon]]}}~~
−	~~=The [[PhoP regulon]]=~~
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU29110
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29110&redirect=T BSU29110]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoPR.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10363]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' [[transcription factors of the OmpR family\|OmpR family]] of two-component response regulators
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:''' phosphorylation by [[PhoR]] under conditions of phosphate limitation (stimulates DNA-binding activity)
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:''' phosphorylation stimulates DNA-binding activity
−
−	* '''[[SubtInteract\|Interactions]]:''' [[PhoP]]-[[PhoP]], [[PhoP]]-[[PhoR]]
−
−	* '''[[Localization]]:''' cell membrane (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29110&redirect=T BSU29110]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MVO 1MVO] (receiver domain)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P13792 P13792]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29110]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[phoP]]-[[phoR]]'' {{PubMed\|14762014}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=phoP_2977800_2978522_-1 phoP] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|16452408}}, [[SigB]] {{PubMed\|15205429}}, [[SigE]] {{PubMed\|15699190,15205429}}
−
−	* '''Regulation:'''
−	** carbon catabolite repression ([[CcpA]]) {{PubMed\|16452408,12850135}}
−	** expressed under conditions of phosphate limitation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15205429,14762014 PubMed]
−	** expressed in post-exponential phase ([[ScoC]]) {{PubMed\|20382764}}
−
−	* '''Regulatory mechanism:'''
−	** [[CcpA]]: transcription repression {{PubMed\|16452408,12850135}}
−	** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/15205429,14762014 PubMed]
−	** [[ScoC]]: transcription repression {{PubMed\|20382764}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 90 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 706 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A966 ( ''phoP''::''tet''), {{PubMed\|14973033}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A966&Search=1A966 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	~~[[Marion Hulett]], University of Illinois at Chicago, USA [http://www.uic.edu/depts/bios/faculty/hulett/hulettm.shtml Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Regulation of ''[[phoP]]-[[phoR]]'' expression==~~
−	~~<pubmed>20382764 14762014,12850135,15205429,16452408,</pubmed>~~
−	~~==Biochemical analyses==~~
−	~~<pubmed>9680208, 9611818,12486063, 20167622 10433720, 17085571,14973033,12486062,</pubmed>~~
−	~~==Targets of PhoR==~~
−	~~'''Additional publications:''' {{PubMed\|21636651}}~~
−	~~<pubmed>20059685 16030210, 10913081,10094677,9683503,9988472,9457886,9335276,9593301,9098050,</pubmed>~~
−
−	~~==Other original publications==~~
−	~~<pubmed>10094672, 15576792,</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 1: / Line 1: @@
-* '''Description:''' [[two-component systems|two-component]] response regulator, regulation of phosphate metabolism <br/><br/>
+* '''Description:''' [[two-component systems|two-component]] response regulator ([[transcription factors of the OmpR family|OmpR family]]), regulation of phosphate metabolism <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] response regulator
+|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] response regulator ([[transcription factors of the OmpR family|OmpR family]])
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || regulation of [[phosphate metabolism]] <br/>(''[[phoA]], [[phoB]], [[phoD]], [[resA | resABCDE]], [[tagA]]-[[tagB]], [[tagD | tagDEF]], [[tuaA | tuaA-H]]'')
@@ Line 41: / Line 41: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 85: / Line 81: @@
 * '''Catalyzed reaction/ biological activity:'''
-* '''Protein family:'''
+* '''Protein family:''' [[transcription factors of the OmpR family|OmpR family]] of two-component response regulators
 * '''Paralogous protein(s):'''

← Older revision		Revision as of 09:54, 17 April 2014
Line 136:		Line 136:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 90 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 706 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 71: / Line 71: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoPR.html]
@@ Line 105: / Line 106: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MVO 1MVO] (receiver domain)

@@ 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=PhoP PhoP]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/folate_biosynthesis.html Folate], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=phoP phoP]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 5.068

@@ 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=BSU29110 phoP]
 |-
-|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/PhoP PhoP]
+|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=PhoP PhoP]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/folate_biosynthesis.html Folate], [http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''

@@ Line 33: / Line 33: @@
   <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=phoP_2977800_2978522_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:phoP_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=phoP_2977800_2978522_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:phoP_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29110]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoR]]'', ''[[mdh]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29110 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29110 DNA_with_flanks]
 |-
 |-

← Older revision		Revision as of 12:30, 19 September 2012
Line 138:		Line 138:

	* '''Mutant:'''		* '''Mutant:'''
		+	** 1A966 ( ''phoP''::''tet''), {{PubMed\|14973033}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A966&Search=1A966 BGSC]

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