PhoD - Revision history

Jstuelk: /* Original publications */

2015-02-11T13:11:37Z

‎Original publications

Jstuelk: /* Extended information on the protein */

2014-09-19T08:21:51Z

‎Extended information on the protein

Jstuelk at 08:21, 19 September 2014

2014-09-19T08:21:16Z

Jstuelk at 08:19, 19 September 2014

2014-09-19T08:19:03Z

134.76.70.252 at 11:45, 8 April 2014

2014-04-08T11:45:01Z

134.76.38.147 at 12:54, 2 April 2014

2014-04-02T12:54:54Z

Jstuelk at 14:11, 6 December 2013

2013-12-06T14:11:19Z

134.76.70.252 at 15:07, 11 November 2013

2013-11-11T15:07:38Z

134.76.70.252 at 12:28, 16 May 2013

2013-05-16T12:28:28Z

134.76.70.252 at 09:24, 14 May 2013

2013-05-14T09:24:11Z

← Older revision		Revision as of 13:11, 11 February 2015
Line 1:		Line 1:
−	* '''Description:~~''' phosphodiesterase/alkaline phosphatase <br/><br/>~~	+	{{#bank: PhoD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''phoD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ycbS ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| phosphodiesterase/alkaline phosphatase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| aquisition of phosphate upon phosphoate starvation~~
−	\|-
−	\|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=BSU02620 phoD]
−	\|-
−	\|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=PhoD PhoD]
−	\|-
−	\|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=PhoD PhoD]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 62 kDa, 8.394~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1668 bp, 556 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yczK]]'', ''[[tatAD]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02620 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:phoD_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=phoD_284011_285762_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:phoD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02620]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[phosphate metabolism]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[PhoP regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU02620
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU02620&redirect=T BSU02620]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11174]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' A phosphate monoester + H<sub>2</sub>O = an alcohol + phosphate (according to Swiss-Prot)
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−	** one Fe<sup>3+</sup> and two Ca<sup>2+</sup> {{PubMed\|25217636}}
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[TatAD]]-[[PhoD]] {{PubMed\|12867413}}
−
−	* '''[[Localization]]:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], secreted by the [[TatAD]]-[[TatCD]] complex [http://www.ncbi.nlm.nih.gov/sites/entrez/19395490 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU02620&redirect=T BSU02620]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=2YEQ 2YEQ] {{PubMed\|25217636}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P42251 P42251]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU02620]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.1 3.1.3.1]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[phoD]]-[[tatAD]]-[[tatCD]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=phoD_284011_285762_1 phoD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|10094677}}
−
−	* '''Regulation:'''
−	** expressed under conditions of phosphate limitation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094677 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/10094677 PubMed]
−
−	* '''Additional information:'''
−	** expression of the operon depends on functional [[HemAT]] and [[CsbC]] {{PubMed\|23180473}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Oscar Kuipers]], University of Groningen, The Netherlands~~
−	~~[http://molgen.biol.rug.nl/molgen/index.php Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~== Reviews ==~~
−	~~<pubmed> 24140208 </pubmed>~~
−	~~== Original publications ==~~
−	~~<pubmed>8760916,10913081,12867413,10094677,12218047,10556724,19180538,10094677, 18957862, 19383693, 19395490 22960285 22383849 23180473 25217636 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 83: / Line 83: @@
 * '''[[Cofactors]]:'''
-** one Fe and two Ca {{PubMed|25217636}}
+** one Fe<sup>3+</sup> and two Ca<sup>2+</sup> {{PubMed|25217636}}
 * '''Effectors of protein activity:'''

@@ Line 82: / Line 82: @@
 * '''Modification:'''
 * '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 94: / Line 95: @@
 * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU02620&redirect=T BSU02620]
-* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=2YEQ 2YEQ]
+* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=2YEQ 2YEQ] {{PubMed|25217636}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P42251 P42251]

@@ Line 63: / Line 63: @@
 === Additional information===
 =The protein=
@@ Line 149: / Line 146: @@
 <pubmed> 24140208 </pubmed>
 == Original publications ==
-<pubmed>8760916,10913081,12867413,10094677,12218047,10556724,19180538,10094677, 18957862, 19383693, 19395490 22960285 22383849 23180473</pubmed>
+<pubmed>8760916,10913081,12867413,10094677,12218047,10556724,19180538,10094677, 18957862, 19383693, 19395490 22960285 22383849 23180473 25217636 </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=PhoD PhoD]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[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=PhoD PhoD]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 8.394

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoD.html]
@@ Line 94: / Line 95: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=2YEQ 2YEQ]

@@ Line 80: / Line 80: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 144: / Line 144: @@
 =References=
-Additional publications: {{PubMed|22960285}}
+== Reviews ==
-<pubmed>8760916,10913081,12867413,10094677,12218047,10556724,19180538,10094677, 18957862, 19383693, 19395490 22383849 23180473</pubmed>
+<pubmed> 24140208 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=BSU02620 phoD]
 |-
-|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/PhoD PhoD]
+|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=PhoD PhoD]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/wiki/index.php/Protein_secretion Protein secretion]'''

@@ 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=phoD_284011_285762_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:phoD_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=phoD_284011_285762_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:phoD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02620]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yczK]]'', ''[[tatAD]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02620 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02620 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:phoD_context.gif]]