AppB - Revision history

Jstuelk at 08:59, 30 July 2015

2015-07-30T08:59:44Z

Jstuelk at 08:51, 20 July 2015

2015-07-20T08:51:01Z

134.76.70.252 at 09:57, 17 April 2014

2014-04-17T09:57:14Z

134.76.38.147 at 13:24, 2 April 2014

2014-04-02T13:24:37Z

134.76.70.252 at 10:30, 7 January 2014

2014-01-07T10:30:50Z

134.76.70.252 at 16:00, 11 November 2013

2013-11-11T16:00:11Z

134.76.70.252 at 12:58, 16 May 2013

2013-05-16T12:58:28Z

134.76.70.252 at 09:54, 14 May 2013

2013-05-14T09:54:27Z

134.76.70.252 at 12:32, 13 May 2013

2013-05-13T12:32:26Z

Awiechert at 08:19, 30 November 2012

2012-11-30T08:19:52Z

← Older revision		Revision as of 08:59, 30 July 2015
Line 1:		Line 1:
−	* '''Description:''' oligopeptide [[ABC transporter]] (permease) <br/><br/>	+	{{#bank: AppB}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''appB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| oligopeptide [[ABC transporter]] (permease))~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| uptake of oligopeptides~~
−	\|-
−	\|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=BSU11390 appB]
−	\|-
−	~~\|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=AppB~~ AppB]
−	\|-
−	\|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=appB appB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 35 kDa, 9.772~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 951 bp, 317 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[appA/2]]'', ''[[appC]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU11390 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU11390 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU11390 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:appB_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=appB_1215243_1216193_1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:appB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU11390]]~~
−	\|-
−	\|}

−	~~__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 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\|[[ScoC regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU11390
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU11390&redirect=T BSU11390]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/appDFABC.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11088]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' ABC transmembrane type-1 domain (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** ([[AppD]]-[[AppF]])-([[AppB]]-[[AppC]])-[[AppA]] {{PubMed\|10092453}}
−
−	* '''[[Localization]]:''' cell membrane {{PubMed\|10092453}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU11390&redirect=T BSU11390]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P42062 P42062]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU11390]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[appD]]-[[appF]]-[[appA]]-[[appB]]-[[appC]]'' {{PubMed\|7997159}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=appB_1215243_1216193_1 appB] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−	** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 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:'''
−	** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 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): 124 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** GP2100 (D(''[[appD]]-[[appF]]-[[appA]]-[[appB]]-[[appC]]'')::''spc''), 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>12618455,7997159,10092453,,10383984,12618455,12107147, </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 40: / Line 40: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 71: / Line 67: @@
 === Additional information===
 =The protein=
@@ Line 137: / Line 130: @@
 * '''Mutant:'''
 * '''Expression vector:'''

← Older revision		Revision as of 09:57, 17 April 2014
Line 132:		Line 132:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 124 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 64: / Line 64: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/appDFABC.html]
@@ Line 102: / Line 103: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 17: / Line 17: @@
 |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=AppB AppB]
 |-
-|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=appB appB]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 9.772

@@ Line 15: / Line 15: @@
 |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=BSU11390 appB]
 |-
-|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/AppB AppB]
+|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=AppB AppB]
 |-
 |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 32: / Line 32: @@
   <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=appB_1215243_1216193_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:appB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=appB_1215243_1216193_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:appB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU11390]]
 |-
 |}

@@ Line 25: / Line 25: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[appA/2]]'', ''[[appC]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU11390 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU11390 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU11390 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU11390 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU11390 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU11390 DNA_with_flanks]
 |-
 |-

@@ Line 23: / Line 23: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 951 bp, 317 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[appA]]'', ''[[appC]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[appA/2]]'', ''[[appC]]''
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12996&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''