Hom - Revision history

Jstuelk at 11:04, 30 July 2015

2015-07-30T11:04:35Z

Jstuelk at 09:35, 30 July 2015

2015-07-30T09:35:40Z

Jstuelk: /* References */

2015-03-18T17:23:00Z

‎References

134.76.70.252 at 14:08, 17 April 2014

2014-04-17T14:08:36Z

134.76.70.252 at 09:26, 17 April 2014

2014-04-17T09:26:19Z

134.76.38.147 at 14:40, 2 April 2014

2014-04-02T14:40:26Z

Jstuelk at 16:32, 5 March 2014

2014-03-05T16:32:23Z

134.76.70.252 at 11:36, 7 January 2014

2014-01-07T11:36:05Z

Jstuelk at 14:06, 22 December 2013

2013-12-22T14:06:24Z

134.76.70.252 at 14:29, 16 May 2013

2013-05-16T14:29:16Z

← Older revision		Revision as of 11:04, 30 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' homoserine dehydrogenase (NADPH) <br/><br/>~~	+	{{#bank: Hom}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''hom''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| homoserine dehydrogenase (NADPH)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| biosynthesis of methionine and threonine~~
−	\|-
−	\|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=BSU32260 hom]
−	\|-
−	\|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=hom hom]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 47 kDa, 4.9~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1299 bp, 433 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[thrC]]'', ''[[yutH]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU32260 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU32260 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU32260 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:hom_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=hom_3314828_3316129_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:hom_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU32260]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[biosynthesis/ acquisition of amino acids]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU32260
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU32260&redirect=T BSU32260]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10460]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' L-homoserine + NAD(P)<sup>+</sup> = L-aspartate 4-semialdehyde + NAD(P)H (according to Swiss-Prot)
−
−	* '''Protein family:''' homoserine dehydrogenase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:''' subject to feedback inhibition [http://www.ncbi.nlm.nih.gov/sites/entrez/19258532 PubMed]
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU32260&redirect=T BSU32260]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2EJW 2EJW] (from ''Thermus thermophilus hb8'', 37% identity, 57% similarity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P19582 P19582]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32260]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.3 1.1.1.3]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[hom]]-[[thrC]]-[[thrB]]'' {{PubMed\|12107147}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hom_3314828_3316129_-1 hom] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** repressed by casamino acids {{PubMed\|12107147}}
−	** repressed during growth in the presence of branched chain amino acids ([[CodY]]) {{PubMed\|24163341}}
−
−	* '''Regulatory mechanism:'''
−	** [[CodY]]: transcription repression {{PubMed\|24163341}}
−
−	* '''Additional information:'''
−	** subject to feedback inhibition [http://www.ncbi.nlm.nih.gov/sites/entrez/19258532 PubMed]
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 2167 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 1723 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 3436 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2047 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3239 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>12107147 18763711 3139660, 19258532 24163341 25777134 15378759 25755103</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 146: / Line 146: @@
 =References=
-<pubmed>12107147 18763711 3139660, 19258532 24163341 25777134 15378759</pubmed>
+<pubmed>12107147 18763711 3139660, 19258532 24163341 25777134 15378759 25755103</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 146: / Line 146: @@
 =References=
-<pubmed>12107147 18763711 3139660, 19258532 24163341 15378759</pubmed>
+<pubmed>12107147 18763711 3139660, 19258532 24163341 25777134 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 123: / Line 123: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 2167 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 1723 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 121: / Line 121: @@
 ** subject to feedback inhibition [http://www.ncbi.nlm.nih.gov/sites/entrez/19258532 PubMed]
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 91: / Line 92: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2EJW 2EJW] (from ''Thermus thermophilus hb8'', 37% identity, 57% similarity)

@@ Line 41: / Line 41: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},
-{{SubtiWiki category|[[membrane proteins]]}}
+{{SubtiWiki category|[[membrane proteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 115: / Line 116: @@
 ** [[CodY]]: transcription repression {{PubMed|24163341}}
-* '''Additional information:'''  subject to feedback inhibition [http://www.ncbi.nlm.nih.gov/sites/entrez/19258532 PubMed]
+* '''Additional information:'''
 =Biological materials =
@@ Line 137: / Line 140: @@
 =References=
-<pubmed>12107147 18763711 3139660, 19258532 24163341</pubmed>
+<pubmed>12107147 18763711 3139660, 19258532 24163341 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=BSU32260 hom]
 |-
-|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/lys_threo.html Lys, Thr]'''
+|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=hom hom]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.9

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 48: / Line 44: @@
 = This gene is a member of the following [[regulons]] =
+{{SubtiWiki regulon|[[CodY regulon]]}}
 =The gene=
@@ Line 65: / Line 61: @@
 === Additional information===
 =The protein=
@@ Line 83: / Line 76: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:''' subject to feedback inhibition [http://www.ncbi.nlm.nih.gov/sites/entrez/19258532 PubMed]
@@ Line 113: / Line 106: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hom_3314828_3316129_-1 hom] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
 ** repressed by casamino acids {{PubMed|12107147}}
 * '''Regulatory mechanism:'''
 * '''Additional information:'''  subject to feedback inhibition [http://www.ncbi.nlm.nih.gov/sites/entrez/19258532 PubMed]
@@ Line 142: / Line 137: @@
 =References=
-<pubmed>12107147 18763711 3139660, 19258532 </pubmed>
+<pubmed>12107147 18763711 3139660, 19258532 24163341</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=hom_3314828_3316129_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:hom_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hom_3314828_3316129_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:hom_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU32260]]
 |-
 |}