CheY - Revision history

Jstuelk: /* Biological materials */

2015-07-03T14:43:57Z

‎Biological materials

Atkovacs at 13:01, 2 July 2015

2015-07-02T13:01:12Z

Jstuelk: /* Expression and regulation */

2015-02-12T14:16:56Z

‎Expression and regulation

Jstuelk at 15:46, 29 December 2014

2014-12-29T15:46:40Z

134.76.70.252 at 09:33, 17 April 2014

2014-04-17T09:33:14Z

Jstuelk: /* The protein */

2014-04-14T13:34:18Z

‎The protein

Jstuelk: /* Database entries */

2014-04-14T13:33:47Z

‎Database entries

134.76.38.147 at 13:44, 2 April 2014

2014-04-02T13:44:02Z

134.76.70.252 at 16:17, 11 November 2013

2013-11-11T16:17:48Z

134.76.70.252 at 13:22, 16 May 2013

2013-05-16T13:22:17Z

← Older revision		Revision as of 14:43, 3 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' [[two-component systems\|two-component]] response regulator, modulation of flagellar switch bias <br/><br/>~~	+	{{#bank: CheY}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''cheY''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''cheB ''~~
−	\|-
−	~~\|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"\|'''Function''' \|\| modulation of flagellar switch bias~~
−	\|-
−	\|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=BSU16330 cheY]
−	\|-
−	\|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=CheY CheY]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 13 kDa, 4.746~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 360 bp, 120 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[fliY]]'', ''[[fliZ]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16330 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:cheY_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=cheY_1703834_1704196_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:cheY_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16330]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[motility and chemotaxis]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[DegU regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigD regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU16330
−
−	~~===Phenotypes of a mutant ===~~
−	* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed\|26122431}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16330&redirect=T BSU16330]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10258]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[YneI]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−	** phosphorylated by [[CheA]] on an Asp residue
−	** dephosphorylated by [[CheC]] {{PubMed\|23226535}}
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[CheY]]-P-[[CheC]] {{PubMed\|23226535}}
−	** [[CheA]]-[[CheY]]
−
−	* '''[[Localization]]:'''
−	** cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16330&redirect=T BSU16330]
−
−	* '''Structure:''' [http://pdb.org/pdb/explore/explore.do?structureId=1tmy 1TMY] ([[CheY]] from ''Thermotoga maritima'')
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P24072 P24072]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16330]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' part of the [[fla-che operon]]
−	** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed\|9657996,8157612,15175317}}
−	** ''[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed\|20233303}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cheY_1703834_1704196_1 cheY] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−	** ''[[flgB]]'': [[SigA]] {{PubMed\|9657996}}, [[SigD]] {{PubMed\|9657996}}
−	** ''[[ylxF]]'': [[SigD]] {{PubMed\|20233303}}
−
−	* '''Regulation:''' see [[fla-che operon]]
−
−	* '''Regulatory mechanism:''' see [[fla-che operon]]
−
−	* '''Additional information:'''
−	** in minimal medium, CheY is present with 7,100 +/- 1,000 molecules per cell {{PubMed\|21515776}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1164 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 2117 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A798 ( ''cheY''::''cat''), {{PubMed\|1905718}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A798&Search=1A798 BGSC]
−	** DS6870 (marker-less in NCIB3610) {{PubMed\|25313396}}
−	** TB191 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed\|26122431}}
−	** TB207 ''amyE''::Phy-''mKATE2'' (marker-less in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed\|26122431}}
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>25313396, 26122431, 19494578,,10094672 20122866 16224120 </pubmed>~~
−
−	~~==Original Publications==~~
−	~~<pubmed>,17908686,10196193,17850253,12920116,8369293,9194713,14651647, 9657996,8157612,15175317, 14749334,20080618,17675386 21515776 24386445</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 57: / Line 57: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 135: / Line 136: @@
 * '''Mutant:'''
 ** 1A798 ( ''cheY''::''cat''), {{PubMed|1905718}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A798&Search=1A798 BGSC]
 * '''Expression vector:'''
@@ Line 152: / Line 156: @@
 =References=
 ==Reviews==
-<pubmed>19494578,,10094672 20122866  16224120 </pubmed>
+<pubmed>25313396, 26122431, 19494578,,10094672 20122866  16224120 </pubmed>
 ==Original Publications==

@@ Line 112: / Line 112: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''' part of the [[fla-che operon]]
 ** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}}
 ** ''[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|20233303}}
@@ Line 122: / Line 122: @@
 ** ''[[ylxF]]'': [[SigD]] {{PubMed|20233303}}
-* '''Regulation:'''
+* '''Regulation:''' see [[fla-che operon]]
-* '''Regulatory mechanism:'''
+* '''Regulatory mechanism:''' see [[fla-che operon]]
 * '''Additional information:'''

@@ Line 46: / Line 46: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[CodY regulon]]}},
 {{SubtiWiki regulon|[[SigD regulon]]}},
 {{SubtiWiki regulon|[[Spo0A regulon]]}}
@@ Line 128: / Line 129: @@
 ** [[CodY]]: transcription repression {{PubMed|12730172}}
 ** [[DegU]] (non-phosphorylated): transcription activation {{PubMed|17850253}}
 * '''Additional information:'''
@@ Line 158: / Line 161: @@
 ==Original Publications==
-<pubmed>,17908686,10196193,17850253,12920116,8369293,9194713,14651647, 9657996,8157612,15175317, 14749334,20080618,17675386 21515776</pubmed>
+<pubmed>,17908686,10196193,17850253,12920116,8369293,9194713,14651647, 9657996,8157612,15175317, 14749334,20080618,17675386 21515776 24386445</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 131: / Line 131: @@
 * '''Additional information:'''
 ** in minimal medium, CheY is present with 7,100 +/- 1,000 molecules per cell {{PubMed|21515776}}
 =Biological materials =

@@ Line 74: / Line 74: @@
 * '''Protein family:'''
-* '''Paralogous protein(s):'''
+* '''Paralogous protein(s):''' [[YneI]]
 === Extended information on the protein ===
@@ Line 80: / Line 80: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
@@ Line 86: / Line 86: @@
 ** dephosphorylated by [[CheC]] {{PubMed|23226535}}
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''

@@ Line 100: / Line 100: @@
 * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16330&redirect=T BSU16330]
-* '''Structure:'''
+* '''Structure:'''	[http://pdb.org/pdb/explore/explore.do?structureId=1tmy 1TMY] ([[CheY]] from ''Thermotoga maritima'')
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P24072 P24072]

@@ 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=BSU16330 cheY]
 |-
-|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/CheY CheY]
+|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=CheY CheY]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 4.746

@@ Line 29: / Line 29: @@
   <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=cheY_1703834_1704196_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cheY_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cheY_1703834_1704196_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cheY_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16330]]
 |-
 |}