RocD - Revision history

134.76.70.252 at 14:13, 17 April 2014

2014-04-17T14:13:44Z

134.76.70.252 at 09:57, 17 April 2014

2014-04-17T09:57:02Z

134.76.38.147 at 15:16, 2 April 2014

2014-04-02T15:16:28Z

134.76.70.252 at 12:03, 7 January 2014

2014-01-07T12:03:51Z

Jstuelk at 07:37, 23 July 2013

2013-07-23T07:37:59Z

134.76.70.252 at 15:01, 16 May 2013

2013-05-16T15:01:34Z

134.76.70.252 at 11:44, 14 May 2013

2013-05-14T11:44:14Z

134.76.70.252 at 14:19, 13 May 2013

2013-05-13T14:19:07Z

134.76.70.252 at 17:47, 7 August 2012

2012-08-07T17:47:31Z

134.76.70.252 at 12:59, 23 April 2012

2012-04-23T12:59:51Z

← Older revision		Revision as of 14:13, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' ornithine transaminase <br/><br/>~~	+	{{#bank: RocD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''rocD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| ornithine transaminase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| arginine, ornithine and citrulline utilization~~
−	\|-
−	\|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=BSU40340 rocD]
−	\|-
−	\|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=rocD rocD]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 43 kDa, 4.894~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1203 bp, 401 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[rocE]]'', ''[[rocR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40340 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40340 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40340 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:rocD_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=rocD_4144301_4145506_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:rocD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40340]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[utilization of amino acids]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AhrC regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[RocR regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigL regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU40340
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40340&redirect=T BSU40340]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocDEF.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10722]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid (according to Swiss-Prot)
−
−	* '''Protein family:''' OAT subfamily (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40340&redirect=T BSU40340]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3RUY 3RUY] (from ''B. anthracis'')
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P38021 P38021]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40340]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/2.6.1.13 2.6.1.13]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[rocD]]-[[rocE]]-[[rocF]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rocD_4144301_4145506_-1 rocD] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]
−
−	* '''Regulation:'''
−	** induced by arginine ([[RocR]], [[AhrC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]
−	** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−	** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[RocR]], [[AhrC]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]
−	** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−	** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 337 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 113714 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP656, aphA3, available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>12618455,23869754,14651647,12618455,7540694, </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 125: / Line 125: @@
 ** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
 * '''Additional information:'''
 =Biological materials =

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocDEF.html]
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3RUY 3RUY] (from ''B. anthracis'')

@@ 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=BSU40340 rocD]
 |-
-|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/glutamate.html Ammonium/ glutamate]'''
+|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=rocD rocD]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 4.894

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 115: / Line 111: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rocD_4144301_4145506_-1 rocD] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]
+* '''[[Sigma factor]]:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694 PubMed]
 * '''Regulation:'''
@@ Line 130: / Line 126: @@
 =Biological materials =
-* '''Mutant:''' GP656, aphA3, available in the [[Stülke]] lab
+* '''Mutant:''' GP656, aphA3, available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''
@@ Line 148: / Line 144: @@
 =References=
-<pubmed>12618455,,14651647,12618455,7540694, </pubmed>
+<pubmed>12618455,23869754,14651647,12618455,7540694, </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=rocD_4144301_4145506_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rocD_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rocD_4144301_4145506_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rocD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40340]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocE]]'', ''[[rocR]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40340 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40340 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40340 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40340 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40340 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40340 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:rocD_context.gif]]

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || arginine, ornithine and citrulline utilization
 |-
 |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/glutamate.html Ammonium/ glutamate]'''