PgdS - Revision history

Jstuelk: /* Extended information on the protein */

2015-07-13T08:46:46Z

‎Extended information on the protein

134.76.38.147 at 14:58, 2 April 2014

2014-04-02T14:58:12Z

Jstuelk: /* References */

2014-02-16T12:12:03Z

‎References

Jstuelk: /* References */

2013-12-04T19:47:46Z

‎References

Jstuelk at 19:47, 4 December 2013

2013-12-04T19:47:24Z

134.76.70.252 at 14:44, 16 May 2013

2013-05-16T14:44:15Z

134.76.70.252 at 11:26, 14 May 2013

2013-05-14T11:26:30Z

134.76.70.252 at 14:01, 13 May 2013

2013-05-13T14:01:10Z

Jstuelk: /* References */

2013-01-25T17:39:11Z

‎References

134.76.70.252 at 16:39, 7 August 2012

2012-08-07T16:39:39Z

← Older revision		Revision as of 08:46, 13 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' gamma-DL-glutamyl hydrolase <br/><br/>~~	+	{{#bank: PgdS}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''pgdS''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ywtD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| gamma-DL-glutamyl hydrolase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| polyglutamic acid degradation~~
−	\|-
−	\|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=BSU35860 pgdS]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 45 kDa, 8.52~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1239 bp, 413 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ywtE]]'', ''[[capE]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35860 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35860 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35860 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ywtD_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=pgdS_3696257_3697498_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:pgdS_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35860]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[capsule biosynthesis and degradation]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigD regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU35860
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35860&redirect=T BSU35860]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywtD.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12535]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' nlpC/p60 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]]:''' secreted (according to Swiss-Prot), extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35860&redirect=T BSU35860]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P96740 P96740]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35860]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''pgdS'' {{PubMed\|15033535}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pgdS_3696257_3697498_-1 pgdS] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigD]] {{PubMed\|15033535}}
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:''' available in [[Daniel Kearns]]'s lab {{PubMed\|24296669}}
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~== Reviews ==~~
−	~~<pubmed> 16689787</pubmed>~~
−	~~== Original publications ==~~
−	~~<pubmed>18957862 12644511, 15033535 23335395</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 52: / Line 52: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywtD.html]
@@ Line 89: / Line 90: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 133: / Line 133: @@
 =References=
 <pubmed>18957862 12644511, 15033535 23335395</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 133: / Line 133: @@
 =References=
-'''Additional publications:''' {{PubMed|23335395}}
+<pubmed>18957862 12644511, 15033535 23335395</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 80: / Line 76: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 110: / Line 106: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pgdS_3696257_3697498_-1 pgdS] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigD]] {{PubMed|15033535}}
+* '''[[Sigma factor]]:''' [[SigD]] {{PubMed|15033535}}
 * '''Regulation:'''
@@ Line 124: / Line 120: @@
 * '''Expression vector:'''
-* '''lacZ fusion:'''
+* '''lacZ fusion:''' available in [[Daniel Kearns]]'s lab {{PubMed|24296669}}
 * '''GFP fusion:'''

@@ Line 27: / Line 27: @@
   <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=pgdS_3696257_3697498_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pgdS_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=pgdS_3696257_3697498_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:pgdS_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35860]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywtE]]'', ''[[capE]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35860 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35860 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35860 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35860 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35860 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35860 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ywtD_context.gif]]

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || polyglutamic acid degradation
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU35860 pgdS]
+|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=BSU35860 pgdS]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 8.52
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywtE]]'', ''[[capE]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15603&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35860 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35860 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35860 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ywtD_context.gif]]