CheD - Revision history

Jstuelk: /* Biological materials */

2015-07-03T14:41:06Z

‎Biological materials

Atkovacs at 12:55, 2 July 2015

2015-07-02T12:55:41Z

Jstuelk at 15:58, 3 April 2015

2015-04-03T15:58:23Z

Jstuelk: /* Expression and regulation */

2015-02-12T14:18:20Z

‎Expression and regulation

Jstuelk at 15:52, 29 December 2014

2014-12-29T15:52:52Z

134.76.38.147 at 13:44, 2 April 2014

2014-04-02T13:44:49Z

134.76.70.252 at 16:18, 11 November 2013

2013-11-11T16:18:34Z

134.76.70.252 at 13:23, 16 May 2013

2013-05-16T13:23:08Z

134.76.70.252 at 10:15, 14 May 2013

2013-05-14T10:15:18Z

134.76.70.252 at 12:51, 13 May 2013

2013-05-13T12:51:23Z

← Older revision		Revision as of 14:41, 3 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' chemoreceptor deaminase, required for methylation of methyl-accepting chemotaxis proteins by [[CheR]], enhances phosphatase activity of [[CheC]], required for full [[McpC]] activity <br/><br/>~~	+	{{#bank: CheD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''cheD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ylxK ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| protein deaminase, [[CheC]] activity modulator~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[motility and chemotaxis]]~~
−	\|-
−	\|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=BSU16460 cheD]
−	\|-
−	\|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=CheD CheD]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 17 kDa, 9.347~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 498 bp, 166 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[cheC]]'', ''[[sigD]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16460 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16460 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16460 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:cheD_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=cheD_1715970_1716470_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:cheD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16460]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[protein modification]]}},~~
−	~~{{SubtiWiki category\|[[motility and chemotaxis]]}}~~
−
−	~~= 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:''' BSU16460
−
−	~~===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=BSU16460&redirect=T BSU16460]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10750]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** binds chemoreceptors and increases their ability to activate the kinase activity of [[CheA]] {{PubMed\|23226535}}
−	** Protein L-glutamine + H<sub>2</sub>O = protein L-glutamate + NH<sub>3</sub> (according to Swiss-Prot)
−	** deaminates Gln-586, Gln-593, and Gln594 in [[McpA]] {{PubMed\|22931217}}
−	** deaminates Gln-609 in [[McpC]] {{PubMed\|22931217}}
−
−	* '''Protein family:''' cheD family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[CheC]]-[[CheD]] {{PubMed\|17908686}}, this interaction is enhanced by [[CheY]]-P {{PubMed\|23226535}}
−	** [[CheD]]-[[McpA]], deamination of Gln-586, Gln-593 and Gln-594 in [[McpA]] {{PubMed\|22931217}}
−	** [[CheD]]-[[McpC]], deamination of Gln-609 in [[McpC]] {{PubMed\|22931217}}
−	** [[McpB]]-[[CheD]] to increase the ability of [[McpB]] to activate [[CheA]] {{PubMed\|25039821}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16460&redirect=T BSU16460]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P40404 P40404]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16460]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.1.44 3.5.1.44]
−
−	~~=== 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=cheD_1715970_1716470_1 cheD] {{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, CheD is present with 1,200 +/- 250 molecules per cell {{PubMed\|21515776}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A861 ( ''cheD''::''cat''), {{PubMed\|7893679}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A861&Search=1A861 BGSC]
−	** 1A863 ( ''cheD''::''cat''), {{PubMed\|7893679}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A863&Search=1A863 BGSC]
−	** DS6868 (marker-less in NCIB3610) {{PubMed\|25313396}}
−	** TB190 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed\|26122431}}
−	** TB206 ''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>,18774298,,18990184</pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed> 25313396, 26122431, 17850253 21515776 22931217 23226535 7893679,15317802, 17908686,12011078, 8866475,11722727,9194713, 14651647,9657996,8157612,15175317, 16469702 24386445 25039821</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 56: / Line 56: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 137: / Line 138: @@
 ** 1A861 ( ''cheD''::''cat''), {{PubMed|7893679}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A861&Search=1A861 BGSC]
 ** 1A863 ( ''cheD''::''cat''), {{PubMed|7893679}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A863&Search=1A863 BGSC]
 * '''Expression vector:'''
@@ Line 156: / Line 160: @@
 <pubmed>,18774298,,18990184</pubmed>
 ==Original publications==
-<pubmed>17850253 21515776 22931217 23226535 7893679,15317802, 17908686,12011078, 8866475,11722727,9194713, 14651647,9657996,8157612,15175317, 16469702 24386445 25039821</pubmed>
+<pubmed> 25313396, 26122431, 17850253 21515776 22931217 23226535 7893679,15317802, 17908686,12011078, 8866475,11722727,9194713, 14651647,9657996,8157612,15175317, 16469702 24386445 25039821</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 97: / Line 97: @@
 ** [[CheD]]-[[McpA]], deamination of Gln-586, Gln-593 and Gln-594 in [[McpA]] {{PubMed|22931217}}
 ** [[CheD]]-[[McpC]], deamination of Gln-609 in [[McpC]] {{PubMed|22931217}}
 * '''[[Localization]]:'''
@@ Line 155: / Line 156: @@
 <pubmed>,18774298,,18990184</pubmed>
 ==Original publications==
-<pubmed>17850253 21515776 22931217 23226535 7893679,15317802, 17908686,12011078, 8866475,11722727,9194713, 14651647,9657996,8157612,15175317, 16469702 24386445</pubmed>
+<pubmed>17850253 21515776 22931217 23226535 7893679,15317802, 17908686,12011078, 8866475,11722727,9194713, 14651647,9657996,8157612,15175317, 16469702 24386445 25039821</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 114: / Line 114: @@
 =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 124: / Line 124: @@
 ** ''[[ylxF]]'': [[SigD]] {{PubMed|20233303}}
-* '''Regulation:'''
+* '''Regulation:''' see [[fla-che operon]]
-* '''Regulatory mechanism:'''
+* '''Regulatory mechanism:''' see [[fla-che operon]]
 * '''Additional information:'''

@@ Line 45: / Line 45: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[CodY regulon]]}},
 {{SubtiWiki regulon|[[SigD regulon]]}},
 {{SubtiWiki regulon|[[Spo0A regulon]]}}
@@ Line 130: / Line 131: @@
 ** [[CodY]]: transcription repression {{PubMed|12730172}}
 ** [[DegU]] (non-phosphorylated): transcription activation {{PubMed|17850253}}
 * '''Additional information:'''
@@ Line 158: / Line 161: @@
 <pubmed>,18774298,,18990184</pubmed>
 ==Original publications==
-<pubmed>17850253 21515776</pubmed>
+<pubmed>17850253 21515776 22931217 23226535 7893679,15317802, 17908686,12011078, 8866475,11722727,9194713, 14651647,9657996,8157612,15175317, 16469702 24386445</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
@@ Line 99: / Line 100: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=BSU16460 cheD]
 |-
-|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/CheD CheD]
+|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=CheD CheD]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 9.347

@@ 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=cheD_1715970_1716470_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cheD_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cheD_1715970_1716470_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cheD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16460]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cheC]]'', ''[[sigD]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16460 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16460 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16460 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16460 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16460 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16460 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:cheD_context.gif]]