FrlO - Revision history

Jstuelk: /* Expression and regulation */

2015-05-28T15:34:49Z

‎Expression and regulation

134.76.70.252 at 11:25, 17 April 2014

2014-04-17T11:25:57Z

134.76.38.147 at 14:41, 2 April 2014

2014-04-02T14:41:29Z

134.76.70.252 at 11:37, 7 January 2014

2014-01-07T11:37:04Z

134.76.70.252 at 14:20, 18 November 2013

2013-11-18T14:20:25Z

Jstuelk: /* References */

2013-07-13T16:37:11Z

‎References

134.76.70.252 at 14:30, 16 May 2013

2013-05-16T14:30:28Z

134.76.70.252 at 11:12, 14 May 2013

2013-05-14T11:12:33Z

134.76.70.252 at 13:47, 13 May 2013

2013-05-13T13:47:30Z

Umaeder: /* References */

2012-11-27T18:49:57Z

‎References

← Older revision		Revision as of 15:34, 28 May 2015
Line 1:		Line 1:
−	* '''Description:~~''' aminosugar [[ABC transporter]] (binding protein) <br/><br/>~~	+	{{#bank: FrlO}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''frlO''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' yurO''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| aminosugar [[ABC transporter]] (binding protein)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| uptake of sugar amines~~
−	\|-
−	\|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=BSU32600 frlO]
−	\|-
−	\|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=FrlO FrlO]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=frlO frlO]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 47 kDa, 5.674~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1266 bp, 422 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[frlN]]'', ''[[frlB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU32600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU32600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU32600 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yurO_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=frlO_3349761_3351029_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:frlO_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU32600]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[ABC transporters]]}},~~
−	~~{{SubtiWiki category\|[[utilization of specific carbon sources]]}},~~
−	~~{{SubtiWiki category\|[[utilization of nitrogen sources other than amino acids]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}}, {{SubtiWiki regulon\|[[FrlR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU32600
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU32600&redirect=T BSU32600]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14001]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' bacterial solute-binding protein 1 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]]:'''
−	** [[YurJ]]-([[FrlM]]-[[FrlN]])-[[FrlO]] {{PubMed\|10092453}}
−
−	* '''[[Localization]]:''' membrane associated (via [[FrlM]]-[[FrlN]]) {{PubMed\|10092453,18763711}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU32600&redirect=T BSU32600]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O32156 O32156]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32600]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:'''
−	** ''[[frlB]]-[[frlO]]-[[frlN]]-[[frlM]]-[[frlD]]'' {{PubMed\|23175651,21347729}}
−	** ''[[frlB]]-[[frlO]]'' {{PubMed\|23175651}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=frlO_3349761_3351029_-1 frlO] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−	**'' [[frlB]]'': repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
−	** ''[[frlB]]'': induced in the presence of fructosamine ([[FrlR]]) {{PubMed\|21397556}}
−
−	* '''Regulatory mechanism:'''
−	** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed1], [http://www.ncbi.nlm.nih.gov/sites/entrez/18083814 PubMed2]
−	** [[FrlR]]: transcription repression {{PubMed\|21397556}}
−
−	* '''Additional information:'''
−	** the mRNA is substantially stabilized upon depletion of [[Rny\|RNase Y]] {{PubMed\|21815947}}
−	** the ''[[frlB]]-[[frlO]]-[[frlN]]-[[frlM]]-[[frlD]]'' operon is not expressed in a ''[[cshA]]'' mutant {{PubMed\|23175651}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 696 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed> 23175651 21815947 12618455,10092453, 21347729, 18763711, 21398478</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 130: / Line 130: @@
 ** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}
 ** the ''[[frlB]]-[[frlO]]-[[frlN]]-[[frlM]]-[[frlD]]'' operon is not expressed in a ''[[cshA]]'' mutant {{PubMed|23175651}}
 =Biological materials =

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 97: / Line 98: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 18: / Line 18: @@
 |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=FrlO FrlO]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Alternative nitrogen sources]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=frlO frlO]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 5.674

@@ 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=BSU32600 frlO]
 |-
-|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/FrlO FrlO]
+|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=FrlO FrlO]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/other_nitrogen_sources/index.html Alternative nitrogen sources]'''

@@ Line 148: / Line 148: @@
 =References=
 <pubmed> 23175651 21815947 12618455,10092453, 21347729, 18763711, 21398478</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=frlO_3349761_3351029_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:frlO_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=frlO_3349761_3351029_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:frlO_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU32600]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[frlN]]'', ''[[frlB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU32600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU32600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU32600 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU32600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU32600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU32600 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yurO_context.gif]]

@@ Line 148: / Line 148: @@
 =References=
-'''Additional references:''' {{PubMed|21397556}}
 <pubmed> 23175651 </pubmed>
   <big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J''  </big>