YfkN - Revision history

134.76.38.147 at 13:12, 2 April 2014

2014-04-02T13:12:26Z

134.76.70.252 at 15:25, 11 November 2013

2013-11-11T15:25:41Z

134.76.70.252 at 12:47, 16 May 2013

2013-05-16T12:47:00Z

134.76.70.252 at 09:42, 14 May 2013

2013-05-14T09:42:58Z

134.76.70.252 at 12:21, 13 May 2013

2013-05-13T12:21:52Z

Raphael2215 at 11:18, 13 August 2012

2012-08-13T11:18:36Z

134.76.70.252 at 15:58, 6 August 2012

2012-08-06T15:58:25Z

Jstuelk: /* Categories containing this gene/protein */

2012-07-09T16:32:16Z

‎Categories containing this gene/protein

Jstuelk: /* Extended information on the protein */

2012-07-09T16:27:00Z

‎Extended information on the protein

134.76.70.252 at 16:01, 18 April 2012

2012-04-18T16:01:08Z

← Older revision		Revision as of 13:12, 2 April 2014
Line 1:		Line 1:
−	* '''Description:''' extracellular 2',3' cyclic nucleotide phosphodiesterase, 2' (or 3') nucleotidase and 5' nucleotidase <br/><br/>	+	{{#bank: YfkN}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yfkN''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| 2',3' cyclic nucleotide phosphodiesterase, <br/>2' (or 3') nucleotidase and 5' nucleotidase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| probably phosphate acquisition~~
−	\|-
−	~~\|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=BSU07840 yfkN]~~
−	\|-
−	\|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=YfkN YfkN]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 159 kDa, 5.021~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 4386 bp, 1462 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[hypO]]'', ''[[yfkM]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07840 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07840 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07840 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yfkN_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=yfkN_855114_859502_-1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:yfkN_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07840]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−
−
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[phosphate metabolism]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CcpA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[PhoP regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU07840
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~essential [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]~~
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfkN.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12930]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[YhcR]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:''' [[YhcS]]-[[YfkN]] {{PubMed\|21800427}} (anchoring to the cell wall)
−
−	* '''[[Localization]]:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], the transmembrane domain serves as retention signal, attached to the cell wall {{PubMed\|21800427,22767609}}
−
−	~~=== Database entries ===~~
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3GVE 3GVE]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34313 O34313]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07840]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''yfkN'' {{PubMed\|16291680}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yfkN_855114_859502_-1 yfkN] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−	** repressed by glucose (5.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
−	** expressed under conditions of phosphate limitation ([[PhoP]]) {{PubMed\|16291680}}
−
−	* '''Regulatory mechanism:'''
−	** [[CcpA]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
−	** [[PhoP]]: transcription activation {{PubMed\|16291680}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~'''Additional referencecs:''' {{PubMed\|21906378}}~~
−	~~<pubmed>14688230,,16291680,18957862 12850135 17114254,21800427 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ 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=BSU07840 yfkN]
 |-
-|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/YfkN YfkN]
+|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=YfkN YfkN]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 159 kDa, 5.021

@@ 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=yfkN_855114_859502_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yfkN_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yfkN_855114_859502_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yfkN_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU07840]]
 |-
 |}

@@ Line 23: / Line 23: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hypO]]'', ''[[yfkM]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07840 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07840 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07840 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07840 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07840 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07840 DNA_with_flanks]
 |-
 |-

@@ Line 13: / Line 13: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || probably phosphate acquisition
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU07840 yfkN]
+|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=BSU07840 yfkN]
 |-
 |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/YfkN YfkN]
@@ Line 23: / Line 23: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hypO]]'', ''[[yfkM]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12613&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU07840 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU07840 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU07840 Advanced_DNA]
 |-
 |-

@@ Line 1: / Line 1: @@
+* '''Description:''' extracellular 2',3' cyclic nucleotide phosphodiesterase, 2' (or 3') nucleotidase and 5' nucleotidase <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-

@@ Line 45: / Line 45: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[phosphate metabolism]]}},
 {{SubtiWiki category|[[membrane proteins]]}}

@@ Line 96: / Line 96: @@
 * '''[[SubtInteract|Interactions]]:''' [[YhcS]]-[[YfkN]] {{PubMed|21800427}} (anchoring to the cell wall)
-* '''[[Localization]]:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], the transmembrane domain serves as retention signal, attached to the cell wall {{PubMed|21800427}}
+* '''[[Localization]]:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], the transmembrane domain serves as retention signal, attached to the cell wall {{PubMed|21800427,22767609}}
 === Database entries ===