PdeH - Revision history

134.76.70.252 at 11:39, 8 April 2014

2014-04-08T11:39:30Z

Jstuelk: /* Biological materials */

2013-08-13T14:20:06Z

‎Biological materials

Aklewing: /* Biological materials */

2013-08-13T11:36:52Z

‎Biological materials

Jstuelk: /* The protein */

2013-08-10T10:40:51Z

‎The protein

Jstuelk at 10:39, 10 August 2013

2013-08-10T10:39:50Z

Jstuelk at 10:22, 10 August 2013

2013-08-10T10:22:13Z

Jstuelk: Jstuelk moved page YuxH to PdeH: 23893111

2013-08-10T10:20:38Z

Jstuelk moved page YuxH to PdeH: 23893111

Jstuelk: /* References */

2013-06-19T10:20:10Z

‎References

134.76.70.252 at 14:27, 16 May 2013

2013-05-16T14:27:50Z

134.76.70.252 at 11:09, 14 May 2013

2013-05-14T11:09:42Z

← Older revision		Revision as of 11:39, 8 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' c-di-GMP degrading phosphodiesterase <br/><br/>~~	+	{{#bank: PdeH}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pdeH''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yuxH, comB, yufA ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| c-di-GMP degrading phosphodiesterase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| degradation of c-di-GMP~~
−	\|-
−	\|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=BSU31740 pdeH]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 47 kDa, 5.36~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1227 bp, 409 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yuzC]]'', ''[[pncB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU31740 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU31740 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU31740 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yuxH_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=yuxH_3258037_3259266_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yuxH_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU31740]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[metabolism of signalling nucleotides]]}},~~
−	~~{{SubtiWiki category\|[[motility and chemotaxis]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU31740
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yuxH.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10377]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** degradation of c-di-GMP {{PubMed\|23893111}}
−
−	* '''Protein family:''' comB family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−	** contains an EAL domain {{PubMed\|22821967}}
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P14203 P14203]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31740]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.71 3.1.3.71]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[pdeH]]'' {{PubMed\|2507523}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yuxH_3258037_3259266_-1 pdeH] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|2507523}}
−
−	* '''Regulation:'''
−	** repressed under conditions that trigger sporulation ([[Spo0A]]) {{PubMed\|14651647,15687200}}
−
−	* '''Regulatory mechanism:'''
−	** [[Spo0A]]: transcription repression {{PubMed\|14651647,15687200}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP1590 (kan) 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>14651647,15687200,2507523 22821967 23893111 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 118: / Line 118: @@
 =Biological materials =
-* '''Mutant:''' GP1590 (kan) available in [[Stülke]] lab
+* '''Mutant:''' GP1590 (kan) available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''

@@ Line 118: / Line 118: @@
 =Biological materials =
-* '''Mutant:'''
+* '''Mutant:''' GP1590 (kan) available in [[Stülke]] lab
 * '''Expression vector:'''

@@ Line 65: / Line 65: @@
 * '''Catalyzed reaction/ biological activity:'''
-** degradation of c-diGMP {{PubMed|23893111}}
+** degradation of c-di-GMP {{PubMed|23893111}}
 * '''Protein family:''' comB family (according to Swiss-Prot)

@@ Line 64: / Line 64: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:''' (2R)-2-phospho-3-sulfolactate + H<sub>2</sub>O = (2R)-3-sulfolactate + phosphate (according to Swiss-Prot)
+* '''Catalyzed reaction/ biological activity:'''
 * '''Protein family:''' comB family (according to Swiss-Prot)

@@ Line 4: / Line 4: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''yuxH''
+|''pdeH''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''comB, yufA ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yuxH, comB, yufA ''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || degradation of c-di-GMP
 |-
-|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=BSU31740 yuxH]
+|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=BSU31740 pdeH]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 5.36
@@ Line 101: / Line 101: @@
 =Expression and regulation=
-* '''Operon:''' ''[[yuxH]]'' {{PubMed|2507523}}
+* '''Operon:''' ''[[pdeH]]'' {{PubMed|2507523}}
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yuxH_3258037_3259266_-1 yuxH] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yuxH_3258037_3259266_-1 pdeH] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|2507523}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2507523}}
 * '''Regulation:'''
@@ Line 134: / Line 134: @@
 =References=
-<pubmed>14651647,15687200,2507523  22821967</pubmed>
+<pubmed>14651647,15687200,2507523  22821967 23893111 </pubmed>
 [[Category:Protein-coding genes]]

← Older revision	Revision as of 10:20, 10 August 2013
(No difference)

@@ 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=yuxH_3258037_3259266_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yuxH_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yuxH_3258037_3259266_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yuxH_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU31740]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yuzC]]'', ''[[pncB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU31740 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU31740 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU31740 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU31740 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU31740 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU31740 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yuxH_context.gif]]