FlgE - Revision history

Jstuelk: /* Biological materials */

2015-07-03T14:46:29Z

‎Biological materials

Atkovacs at 13:10, 2 July 2015

2015-07-02T13:10:40Z

Jstuelk: /* Expression and regulation */

2015-02-12T14:11:22Z

‎Expression and regulation

Jstuelk at 15:43, 29 December 2014

2014-12-29T15:43:07Z

134.76.70.252 at 09:32, 17 April 2014

2014-04-17T09:32:10Z

134.76.38.147 at 13:43, 2 April 2014

2014-04-02T13:43:49Z

134.76.70.252 at 13:22, 16 May 2013

2013-05-16T13:22:01Z

134.76.70.252 at 10:14, 14 May 2013

2013-05-14T10:14:17Z

134.76.70.252 at 12:50, 13 May 2013

2013-05-13T12:50:27Z

Awiechert at 10:01, 3 December 2012

2012-12-03T10:01:25Z

← Older revision		Revision as of 14:46, 3 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' flagellar hook protein <br/><br/>~~	+	{{#bank: FlgE}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''flgE''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''flgG ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| flagellar hook protein~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| movement 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=BSU16290 flgE]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 27 kDa, 4.734~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 792 bp, 264 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[flgD]]'', ''[[ylzI]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16290 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:flgE_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=flgE_1700182_1700976_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:flgE_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16290]]
−	\|-
−	\|}
−
−	~~__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\|[[membrane proteins]]}}~~
−
−	~~= 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:''' BSU16290
−
−	~~===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=BSU16290&redirect=T BSU16290]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10249]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	* lack of [[SigD]]-dependent gene expression (no ''[[hag]]'' expression), no motility {{PubMed\|22730131}}
−
−	* '''Protein family:''' flagella basal body rod proteins family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[FlhO]], [[FlhP]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:''' bacterial flagellum basal body (according to Swiss-Prot), extracellular (no signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16290&redirect=T BSU16290]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P23446 P23446]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16290]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' part of the [[fla-che operon]] (see there for regulation)
−	** ''[[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=flgE_1700182_1700976_1 flgE] {{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:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1780 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3035 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** DS4681 (marker-less in NCIB3610) {{PubMed\|22730131}}
−	** TB187 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed\|26122431}}
−	** TB203 ''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=~~
−	~~<pubmed> 26122431, 14651647,18957862 18763711, 9657996,8157612,15175317 17850253 24386445 22730131</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 56: / Line 56: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 131: / Line 132: @@
 * '''Mutant:'''
 * '''Expression vector:'''
@@ Line 147: / Line 151: @@
 =References=
-<pubmed>14651647,18957862 18763711, 9657996,8157612,15175317 17850253 24386445 22730131</pubmed>
+<pubmed> 26122431, 14651647,18957862 18763711, 9657996,8157612,15175317 17850253 24386445 22730131</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 110: / Line 110: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''' part of the [[fla-che operon]] (see there for regulation)
 ** ''[[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 120: / Line 120: @@
 ** ''[[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 126: / Line 127: @@
 ** [[CodY]]: transcription repression {{PubMed|12730172}}
 ** [[DegU]] (non-phosphorylated): transcription activation {{PubMed|17850253}}
 * '''Additional information:'''
@@ Line 150: / Line 153: @@
 =References=
-'''Additional publications:''' {{PubMed|22730131}}
+<pubmed>14651647,18957862 18763711, 9657996,8157612,15175317 17850253 24386445 22730131</pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 09:32, 17 April 2014
Line 128:		Line 128:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1780 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3035 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=flgE_1700182_1700976_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:flgE_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=flgE_1700182_1700976_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:flgE_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16290]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[flgD]]'', ''[[ylzI]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16290 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16290 DNA_with_flanks]
 |-
 |-

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || movement and chemotaxis
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16290 flgE]
+|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=BSU16290 flgE]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 4.734
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[flgD]]'', ''[[ylzI]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13502&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16290 Advanced_DNA]
 |-
 |-

@@ Line 20: / Line 20: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[flgD]]'', ''[[fliL]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[flgD]]'', ''[[ylzI]]''
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13502&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''