AspB - Revision history

Jstuelk: /* Expression and regulation */

2015-05-08T14:50:32Z

‎Expression and regulation

Jstuelk at 14:43, 8 May 2015

2015-05-08T14:43:12Z

Jstuelk: /* Expression and regulation */

2015-05-07T13:26:25Z

‎Expression and regulation

134.76.70.252 at 14:03, 17 April 2014

2014-04-17T14:03:21Z

134.76.70.252 at 13:32, 17 April 2014

2014-04-17T13:32:57Z

134.76.70.252 at 09:28, 17 April 2014

2014-04-17T09:28:52Z

134.76.38.147 at 14:02, 2 April 2014

2014-04-02T14:02:36Z

Jstuelk at 16:33, 5 March 2014

2014-03-05T16:33:54Z

Jstuelk at 16:33, 5 March 2014

2014-03-05T16:33:24Z

134.76.70.252 at 11:04, 7 January 2014

2014-01-07T11:04:11Z

← Older revision		Revision as of 14:50, 8 May 2015
Line 1:		Line 1:
−	* '''Description:~~''' aspartate transaminase <br/><br/>~~	+	{{#bank: AspB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''aspB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| aspartate transaminase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| biosynthesis of aspartate~~
−	\|-
−	\|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=BSU22370 aspB]
−	\|-
−	\|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=aspB aspB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 42 kDa, 5.298~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1179 bp, 393 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[asnS]]'', ''[[tseB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU22370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU22370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU22370 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:aspB_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=aspB_2347660_2348841_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:aspB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU22370]]
−	\|-
−	\|}
−
−	~~__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]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU22370
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU22370&redirect=T BSU22370]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11513]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate (according to Swiss-Prot)
−
−	* '''Protein family:''' TCR/tet family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU22370&redirect=T BSU22370]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1J32 1J32] (from ''Phormidium lapideum'', 45% identity, 66% similarity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P53001 P53001]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU22370]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/2.6.1.1 2.6.1.1]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ypmB]]-[[aspB]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=aspB_2347660_2348841_-1 aspB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:''' constitutive
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 10916 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 13715 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2849 {{PubMed\|21395229}}
−
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3270 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 7546 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2849 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3270 {{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>15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1179 bp, 393 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[asnS]]'', ''[[ypmB]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[asnS]]'', ''[[tseB]]''
 |-
 |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU22370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU22370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU22370 DNA_with_flanks]

@@ Line 104: / Line 104: @@
 =Expression and regulation=
-* '''Operon:''' ''[[ypmB]]-[[aspB]]''
+* '''Operon:''' ''[[ypmB]]-[[aspB]]'' {{PubMed|22383849}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=aspB_2347660_2348841_-1 aspB] {{PubMed|22383849}}

← Older revision		Revision as of 14:03, 17 April 2014
Line 120:		Line 120:
	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2849 {{PubMed\|21395229}}		** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2849 {{PubMed\|21395229}}

		+	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3270 {{PubMed\|21395229}}
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 7546 {{PubMed\|21395229}}
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2849 {{PubMed\|21395229}}
	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3270 {{PubMed\|21395229}}		** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3270 {{PubMed\|21395229}}

@@ Line 118: / Line 118: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 10916 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 13715 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

@@ Line 116: / Line 116: @@
 * '''Additional information:'''
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 55: / Line 55: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 89: / Line 90: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1J32 1J32] (from ''Phormidium lapideum'', 45% identity, 66% similarity)

@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || aspartate transaminase)
+|style="background:#ABCDEF;" align="center"| '''Product''' || aspartate transaminase
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of aspartate

@@ Line 37: / Line 37: @@
 <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|[[biosynthesis/ acquisition of amino acids]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 64: / Line 61: @@
 === Additional information===
 =The protein=
@@ Line 82: / Line 76: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 112: / Line 106: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=aspB_2347660_2348841_-1 aspB] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:''' constitutive
@@ Line 119: / Line 113: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 139: / Line 134: @@
 =References=
 [[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=BSU22370 aspB]
 |-
-|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/aspartate_asparagine.html Asp, Asn]'''
+|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=aspB aspB]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.298