RibH - Revision history

134.76.70.252 at 09:34, 17 April 2014

2014-04-17T09:34:25Z

134.76.38.147 at 14:06, 2 April 2014

2014-04-02T14:06:25Z

Jstuelk at 09:59, 21 January 2014

2014-01-21T09:59:37Z

134.76.70.252 at 11:07, 7 January 2014

2014-01-07T11:07:27Z

134.76.70.252 at 08:45, 12 November 2013

2013-11-12T08:45:39Z

134.76.70.252 at 13:48, 16 May 2013

2013-05-16T13:48:22Z

134.76.70.252 at 10:36, 14 May 2013

2013-05-14T10:36:58Z

134.76.70.252 at 13:11, 13 May 2013

2013-05-13T13:11:38Z

Jstuelk: /* Expression and regulation */

2013-01-10T20:36:57Z

‎Expression and regulation

Jstuelk at 18:50, 2 January 2013

2013-01-02T18:50:05Z

← Older revision		Revision as of 09:34, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' riboflavin synthase (beta subunit) <br/><br/>~~	+	{{#bank: RibH}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ribH''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| riboflavin synthase (beta subunit)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| riboflavin biosynthesis~~
−	\|-
−	\|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=BSU23250 ribH]
−	\|-
−	\|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=RibH RibH]
−	\|-
−	\|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=ribH ribH]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 16 kDa, 5.196~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 462 bp, 154 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ribT]]'', ''[[ribA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23250 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23250 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23250 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ribH_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=ribH_2427892_2428356_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ribH_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23250]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biosynthesis of cofactors]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[FMN-box]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU23250
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23250&redirect=T BSU23250]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ypuE-ribDEAHT.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10521]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine (according to Swiss-Prot)
−
−	* '''Protein family:''' DMRL synthase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** ([[RibE]])3-([[RibH]])60, the lumazine synthase/riboflavin synthase complex {{PubMed\|7473709}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23250&redirect=T BSU23250]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1zis 1ZIS], [http://www.rcsb.org/pdb/explore.do?structureId=1RVV 1RVV] (the [[RibE]])3-([[RibH]])60 lumazine synthase/riboflavin synthase complex) {{PubMed\|7473709}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P11998 P11998]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23250]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/2.5.1.9 2.5.1.9]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ribD]]-[[ribE]]-[[ribA]]-[[ribH]]-[[ribT]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8159171 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ribH_2427892_2428356_-1 ribH] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|8159171}}
−
−	* '''Regulation:''' expressed in the absence of FMN ([[FMN-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15808508 PubMed]
−
−	* '''Regulatory mechanism:''' [[FMN-box]]: [[riboswitch]], mediates termination/ antitermination control of the operon, in the absence of FMN: antitermination, in the presence of FMN: termination [http://www.ncbi.nlm.nih.gov/sites/entrez/15808508 PubMed]
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>12456892,15808508,7473709, 8159171, 7934830, 3100522 23270261 24442413 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ypuE-ribDEAHT.html]
@@ Line 91: / Line 92: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1zis 1ZIS], [http://www.rcsb.org/pdb/explore.do?structureId=1RVV 1RVV] (the [[RibE]])3-([[RibH]])60 lumazine synthase/riboflavin synthase complex) {{PubMed|7473709}}

@@ Line 62: / Line 62: @@
 === Additional information===
 =The protein=
@@ Line 80: / Line 77: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 111: / Line 108: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ribH_2427892_2428356_-1 ribH] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|8159171}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8159171}}
 * '''Regulation:''' expressed in the absence of FMN ([[FMN-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15808508 PubMed]
@@ Line 139: / Line 136: @@
 =References=
-<pubmed>12456892,15808508,7473709, 8159171, 7934830, 3100522 23270261 </pubmed>
+<pubmed>12456892,15808508,7473709, 8159171, 7934830, 3100522 23270261 24442413 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=RibH RibH]
 |-
-|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/riboflavin.html Riboflavin / FAD]'''
+|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=ribH ribH]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.196

@@ 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=BSU23250 ribH]
 |-
-|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/RibH RibH]
+|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=RibH RibH]
 |-
 |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/riboflavin.html Riboflavin / FAD]'''

@@ 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=ribH_2427892_2428356_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ribH_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ribH_2427892_2428356_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ribH_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23250]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ribT]]'', ''[[ribA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23250 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23250 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23250 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23250 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23250 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23250 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ribH_context.gif]]

@@ Line 107: / Line 107: @@
 =Expression and regulation=
-* '''Operon:'''  ''[[ypuE]]-[[ribD]]-[[ribE]]-[[ribA]]-[[ribH]]-[[ribT]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/8159171 PubMed]
+* '''Operon:'''  ''[[ribD]]-[[ribE]]-[[ribA]]-[[ribH]]-[[ribT]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/8159171 PubMed]
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ribH_2427892_2428356_-1 ribH] {{PubMed|22383849}}

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 143: / Line 139: @@
 =References=
-<pubmed>12456892,15808508,7473709, 8159171, 7934830, 3100522</pubmed>
+<pubmed>12456892,15808508,7473709, 8159171, 7934830, 3100522 23270261 </pubmed>
 [[Category:Protein-coding genes]]