PurL - Revision history

134.76.70.252 at 14:12, 17 April 2014

2014-04-17T14:12:52Z

134.76.70.252 at 09:44, 17 April 2014

2014-04-17T09:44:10Z

134.76.38.147 at 13:08, 2 April 2014

2014-04-02T13:08:08Z

Jstuelk at 16:24, 5 March 2014

2014-03-05T16:24:09Z

134.76.70.252 at 10:17, 7 January 2014

2014-01-07T10:17:02Z

134.76.70.252 at 15:20, 11 November 2013

2013-11-11T15:20:06Z

134.76.70.252 at 12:42, 16 May 2013

2013-05-16T12:42:33Z

134.76.70.252 at 09:37, 14 May 2013

2013-05-14T09:37:51Z

134.76.70.252 at 12:17, 13 May 2013

2013-05-13T12:17:34Z

Raphael2215 at 11:16, 10 August 2012

2012-08-10T11:16:59Z

← Older revision		Revision as of 14:12, 17 April 2014
Line 1:		Line 1:
−	* '''Description:''' phosphoribosylformylglycinamidine synthase <br/><br/>	+	{{#bank: PurL}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''purL''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| phosphoribosylformylglycinamidine synthase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| purine 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=BSU06480 purL]
−	\|-
−	~~\|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=PurL~~ PurL]
−	\|-
−	\|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=purL purL]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 80 kDa, 4.554~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2226 bp, 742 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[purQ]]'', ''[[purF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06480 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06480 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06480 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:purL_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=purL_703237_705465_1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:purL_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU06480]]~~
−	\|-
−	\|}

−	~~__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 nucleotides]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[G-box]]}},~~
−	~~{{SubtiWiki regulon\|[[PurR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU06480
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU06480&redirect=T BSU06480]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/purEKBCSQLFMNHD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10705]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ATP + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H<sub>2</sub>O = ADP + phosphate + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate (according to Swiss-Prot)
−
−	* '''Protein family:''' FGAMS family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[PurS]]-[[PurQ]]-[[PurL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15301530 PubMed]
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU06480&redirect=T BSU06480]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3D54 3D54] (from ''Thermotoga maritima'', 39% identity, 58% similarity) {{PubMed\|18597481}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P12042 P12042]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06480]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/6.3.5.3 6.3.5.3]
−
−	~~=== Additional information===~~
−
−	~~:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]~~
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[purE]]-[[purK]]-[[purB]]-[[purC]]-[[purS]]-[[purQ]]-[[purL]]-[[purF]]-[[purM]]-[[purN]]-[[purH]]-[[purD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=purL_703237_705465_1 purL] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
−
−	* '''Regulation:'''
−	** repressed in the presence of purine nucleotides ([[PurR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
−	** repressed in the presence of adenine or adenosine([[PurR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
−	** repressed in the presence of guanine([[G-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [PurR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
−	** [[PurR]]: transcription repression (molecular inducer: PRPP) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
−	** [[G-box]]: transcription termination/ antitermination ([[riboswitch]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12787499 PubMed2]
−
−	* '''Additional information:'''
−	** subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 3495 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 10654 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>15301530,3036807,12923093,21671997,7638212,18763711 15378759</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 128: / Line 128: @@
 ** subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/purEKBCSQLFMNHD.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3D54 3D54] (from ''Thermotoga maritima'', 39% identity, 58% similarity) {{PubMed|18597481}}

@@ Line 38: / Line 38: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},
-{{SubtiWiki category|[[membrane proteins]]}}
+{{SubtiWiki category|[[membrane proteins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 67: / Line 64: @@
 === Additional information===
 =The protein=
@@ Line 85: / Line 79: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 117: / Line 111: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=purL_703237_705465_1 purL] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
+* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
 * '''Regulation:'''
@@ Line 129: / Line 123: @@
 ** [[G-box]]: transcription termination/ antitermination ([[riboswitch]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12787499 PubMed2]
-* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+* '''Additional information:'''
 =Biological materials =
@@ Line 150: / Line 146: @@
 =References=
-Additional publications: {{PubMed|21671997}}
+<pubmed>15301530,3036807,12923093,21671997,7638212,18763711 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=PurL PurL]
 |-
-|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/purine_biosynthesis.html Purine synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''
+|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=purL purL]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 80 kDa, 4.554

@@ 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=BSU06480 purL]
 |-
-|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/PurL PurL]
+|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=PurL PurL]
 |-
 |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/purine_biosynthesis.html Purine synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''

@@ Line 30: / Line 30: @@
   <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=purL_703237_705465_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:purL_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=purL_703237_705465_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:purL_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU06480]]
 |-
 |}

@@ Line 25: / Line 25: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[purQ]]'', ''[[purF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06480 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06480 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06480 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06480 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06480 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06480 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:purL_context.gif]]

@@ Line 1: / Line 1: @@
+* '''Description:''' phosphoribosylformylglycinamidine synthase <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-