CheB - Revision history

Jstuelk at 14:19, 3 July 2015

2015-07-03T14:19:09Z

Atkovacs at 12:51, 2 July 2015

2015-07-02T12:51:33Z

Atkovacs at 12:50, 2 July 2015

2015-07-02T12:50:24Z

Jstuelk: /* Expression and regulation */

2015-02-12T14:17:51Z

‎Expression and regulation

Jstuelk at 15:49, 29 December 2014

2014-12-29T15:49:58Z

134.76.70.252 at 09:57, 17 April 2014

2014-04-17T09:57:37Z

134.76.38.147 at 13:44, 2 April 2014

2014-04-02T13:44:28Z

134.76.70.252 at 16:18, 11 November 2013

2013-11-11T16:18:10Z

134.76.70.252 at 13:22, 16 May 2013

2013-05-16T13:22:46Z

134.76.70.252 at 10:14, 14 May 2013

2013-05-14T10:14:57Z

← Older revision		Revision as of 14:19, 3 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' MCP-glutamate methylesterase / two-component response regulator-like <br/><br/>~~	+	{{#bank: CheB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''cheB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''cheL ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| MCP-glutamate methylesterase / two-component response regulator-like~~
−	\|-
−	~~\|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=BSU16420 cheB]
−	\|-
−	\|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=CheB CheB]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 38 kDa, 8.119~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1071 bp, 357 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[flhG]]'', ''[[cheA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16420 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16420 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16420 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:cheB_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=cheB_1711736_1712809_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:cheB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16420]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{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:''' BSU16420
−
−	~~===Phenotypes of a mutant ===~~
−	* not essential for pellicle biofilm formation and mutant has similar fitness to the wild-type strain when competed during pellicle formation {{PubMed\|26122431}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16420&redirect=T BSU16420]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10255]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Protein L-glutamate O(5)-methyl ester + H<sub>2</sub>O = protein L-glutamate + methanol (according to Swiss-Prot)
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:''' phosphorylated on a Asp residue by [[CheA]] {{PubMed\|11553614}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16420&redirect=T BSU16420]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/Q05522 Q05522]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16420]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.1.61 3.1.1.61]
−
−	~~=== 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=cheB_1711736_1712809_1 cheB] {{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, CheB is present with 2,100 +/- 400 molecules per cell {{PubMed\|21515776}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 92 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** DS7306 (marker-less in NCIB3610) {{PubMed\|25313396}}
−	** TB194 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed\|26122431}}
−	** TB209 ''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=~~
−	* [[Daniel Kearns]]
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 20122866 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>25313396, 26122431, 10632876,12123464,1905718,14731274,17850253,14651647, 9657996,8157612,15175317 11553614 21515776 24386445</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 132: / Line 132: @@
 * '''Mutant:'''
 ** DS7306 (marker-less in NCIB3610) {{PubMed|25313396}}
-** TB19 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
+** TB194 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
-** TB213 ''amyE''::Phy-''mKATE2'' (marker-less in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}
+** TB209 ''amyE''::Phy-''mKATE2'' (marker-less in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}
 * '''Expression vector:'''

@@ Line 57: / Line 57: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 130: / Line 131: @@
 * '''Mutant:'''
 * '''Expression vector:'''
@@ Line 142: / Line 146: @@
 =Labs working on this gene/protein=
 =Your additional remarks=
@@ Line 149: / Line 154: @@
 <pubmed> 20122866  </pubmed>
 ==Original publications==
-<pubmed>10632876,12123464,1905718,14731274,17850253,14651647, 9657996,8157612,15175317 11553614 21515776 24386445</pubmed>
+<pubmed>25313396, 26122431, 10632876,12123464,1905718,14731274,17850253,14651647, 9657996,8157612,15175317 11553614 21515776 24386445</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 109: / Line 109: @@
 =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 119: / Line 119: @@
 ** ''[[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 125: / Line 126: @@
 ** [[CodY]]: transcription repression {{PubMed|12730172}}
 ** [[DegU]] (non-phosphorylated): transcription activation {{PubMed|17850253}}
 * '''Additional information:'''
@@ Line 152: / Line 155: @@
 <pubmed> 20122866  </pubmed>
 ==Original publications==
-<pubmed>10632876,12123464,1905718,14731274,17850253,14651647, 9657996,8157612,15175317 11553614 21515776</pubmed>
+<pubmed>10632876,12123464,1905718,14731274,17850253,14651647, 9657996,8157612,15175317 11553614 21515776 24386445</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 128: / Line 128: @@
 * '''Additional information:'''
 ** in minimal medium, CheB is present with 2,100 +/- 400 molecules per cell {{PubMed|21515776}}
 =Biological materials =

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
@@ Line 94: / Line 95: @@
 === 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=BSU16420 cheB]
 |-
-|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/CheB CheB]
+|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=CheB CheB]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 38 kDa, 8.119

@@ 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=cheB_1711736_1712809_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cheB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cheB_1711736_1712809_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cheB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16420]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[flhG]]'', ''[[cheA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16420 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16420 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16420 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16420 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16420 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16420 DNA_with_flanks]
 |-
 |-