LdcB - Revision history

Jstuelk at 08:13, 10 June 2014

2014-06-10T08:13:09Z

Jstuelk: /* References */

2014-06-10T08:09:07Z

‎References

Jstuelk at 08:03, 10 June 2014

2014-06-10T08:03:01Z

Jstuelk at 08:00, 10 June 2014

2014-06-10T08:00:47Z

Jstuelk at 07:59, 10 June 2014

2014-06-10T07:59:08Z

Jstuelk: Jstuelk moved page YodJ to LdcB: 24909784

2014-06-10T07:57:47Z

Jstuelk moved page YodJ to LdcB: 24909784

Jstuelk at 07:57, 10 June 2014

2014-06-10T07:57:35Z

134.76.38.147 at 13:56, 2 April 2014

2014-04-02T13:56:00Z

134.76.70.252 at 13:35, 16 May 2013

2013-05-16T13:35:06Z

134.76.70.252 at 10:26, 14 May 2013

2013-05-14T10:26:29Z

← Older revision		Revision as of 08:13, 10 June 2014
Line 1:		Line 1:
−	* '''Description:~~''' LD-carboxypeptidase, releases D-Ala from the cell wall <br/><br/>~~	+	{{#bank: LdcB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ldcB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yodJ ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| LD-carboxypeptidase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[cell wall synthesis]]~~
−	\|-
−	\|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=BSU19620 ldcB]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 30 kDa, 5.84~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 819 bp, 273 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yodI]]'', ''[[deoD]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19620 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yodJ_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=yodJ_2134566_2135387_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yodJ_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19620]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[cell wall synthesis]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU19620
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19620&redirect=T BSU19620]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13538]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** trimming of cell wall peptides (tetrapeptides to tripeptides) wit concomitant release of D-ala {{PubMed\|24909784}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19620&redirect=T BSU19620]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34866 O34866]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19620]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[deoD]]-[[ldcB]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yodJ_2134566_2135387_-1 ldcB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''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=~~
−
−	~~<pubmed>18957862, 24909784 22383849 21378199 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 135: / Line 135: @@
 =References=
-<pubmed>18957862, 24909784 22383849</pubmed>
+<pubmed>18957862, 24909784 22383849 21378199 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 1: / Line 1: @@
-* '''Description:''' LD-carboxypeptidase <br/><br/>
+* '''Description:''' LD-carboxypeptidase, releases D-Ala from the cell wall <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 65: / Line 65: @@
 * '''Catalyzed reaction/ biological activity:'''
-** trimming of cell wall peptides (tetrapeptides to tripeptides) {{PubMed|24909784}}
+** trimming of cell wall peptides (tetrapeptides to tripeptides) wit concomitant release of D-ala {{PubMed|24909784}}
 * '''Protein family:'''

@@ Line 103: / Line 103: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''' ''[[deoD]]-[[ldcB]]'' {{PubMed|22383849}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yodJ_2134566_2135387_-1 ldcB] {{PubMed|22383849}}
@@ Line 135: / Line 135: @@
 =References=
-<pubmed>18957862, 24909784 </pubmed>
+<pubmed>18957862, 24909784 22383849</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || [[cell wall synthesis]]
 |-
-|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=BSU19620 yodJ]
+|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=BSU19620 ldcB]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 5.84
@@ Line 105: / Line 105: @@
 * '''Operon:'''
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yodJ_2134566_2135387_-1 yodJ] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yodJ_2134566_2135387_-1 ldcB] {{PubMed|22383849}}
 * '''[[Sigma factor]]:'''

← Older revision	Revision as of 07:57, 10 June 2014
(No difference)

@@ Line 1: / Line 1: @@
-* '''Description:''' similar to D-alanyl-D-alanine carboxypeptidase <br/><br/>
+* '''Description:''' LD-carboxypeptidase <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''yodJ''
+|''ldcB''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yodJ ''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+|style="background:#ABCDEF;" align="center"| '''Product''' || LD-carboxypeptidase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+|style="background:#ABCDEF;" align="center"|'''Function''' || [[cell wall synthesis]]
 |-
 |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=BSU19620 yodJ]
@@ Line 38: / Line 38: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[cell wall/ other]]}}
+{{SubtiWiki category|[[cell wall synthesis]]}}
 = This gene is a member of the following [[regulons]] =
@@ Line 59: / Line 59: @@
 === Additional information===
 =The protein=
@@ Line 68: / Line 65: @@
 * '''Catalyzed reaction/ biological activity:'''
 * '''Protein family:'''
@@ Line 137: / Line 135: @@
 =References=
-<pubmed>18957862, </pubmed>
+<pubmed>18957862, 24909784 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 52: / Line 52: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 90: / Line 91: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=yodJ_2134566_2135387_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yodJ_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yodJ_2134566_2135387_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yodJ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19620]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yodI]]'', ''[[deoD]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19620 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19620 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yodJ_context.gif]]