YlmE - Revision history

134.76.70.252 at 10:04, 17 April 2014

2014-04-17T10:04:52Z

134.76.38.147 at 13:40, 2 April 2014

2014-04-02T13:40:04Z

Jstuelk at 20:03, 8 March 2014

2014-03-08T20:03:26Z

Jstuelk: /* Basic information/ Evolution */

2013-12-21T18:39:57Z

‎Basic information/ Evolution

Jstuelk at 18:37, 21 December 2013

2013-12-21T18:37:43Z

Jstuelk: /* Database entries */

2013-12-21T18:27:25Z

‎Database entries

Jstuelk at 20:09, 12 November 2013

2013-11-12T20:09:11Z

Jstuelk at 16:47, 4 October 2013

2013-10-04T16:47:30Z

134.76.70.252 at 13:17, 16 May 2013

2013-05-16T13:17:16Z

134.76.70.252 at 10:10, 14 May 2013

2013-05-14T10:10:14Z

← Older revision		Revision as of 10:04, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' enzyme involved in controlling the availability of coenzyme A<br/><br/>~~	+	{{#bank: YlmE}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ylmE''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| unknown~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of the CoA pool~~
−	\|-
−	\|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=BSU15380 ylmE]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 25 kDa, 5.546~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 690 bp, 230 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ylmD]]'', ''[[sepF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15380 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15380 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15380 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ylmE_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=ylmE_1610170_1610862_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ylmE_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15380]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[poorly characterized/ putative enzymes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU15380
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15380&redirect=T BSU15380]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ylmDEFGH.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13374]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** while the protein was described as an amino acid racemase important for biofilm formation {{PubMed\|20431016}}, no racemase activity was detected in ''in vitro'' assays with a functionally active protein {{PubMed\|24097949}}
−
−	* '''Protein family:''' UPF0001 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−	** pyridoxal phosphate {{PubMed\|24097949}}
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15380&redirect=T BSU15380]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1W8G 1W8G] (the structure of YggS from ''E. coli'' 33% identity, 61% similarity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O31727 O31727]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15380]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ylmD]]-[[ylmE]]-[[sepF]]-[[ylmG]]-[[ylmH]]'' {{PubMed\|16420366}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ylmE_1610170_1610862_1 ylmE] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−
−	* '''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>14651647, 16420366 24097949</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 52: / Line 52: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ylmDEFGH.html]
@@ Line 89: / Line 90: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=1W8G 1W8G] (the structure of YggS from ''E. coli'' 33% identity, 61% similarity)

@@ Line 1: / Line 1: @@
-* '''Description:''' putative amino acid racemase, production of D-amino acids, control of [[biofilm formation]] <br/><br/>
+* '''Description:''' enzyme involved in controlling the availability of coenzyme A<br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || putative amino acid racemase
+|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[biofilm formation]]
+|style="background:#ABCDEF;" align="center"|'''Function''' || control of the CoA pool
 |-
 |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=BSU15380 ylmE]
@@ Line 38: / Line 38: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[biofilm formation]]}}
+{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}}
 = This gene is a member of the following [[regulons]] =
@@ Line 136: / Line 136: @@
 =References=
-<pubmed>14651647, 20431016 16420366 24097949</pubmed>
+<pubmed>14651647, 16420366 24097949</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 65: / Line 65: @@
 * '''Catalyzed reaction/ biological activity:'''
-** while the protein was described as an amino acid racemase important for biofilm formation {{PubMed|24097949}}, no racemase activity was detected in in vitro assays with a functionally active protein {{PubMed|24097949}}
+** while the protein was described as an amino acid racemase important for biofilm formation {{PubMed|20431016}}, no racemase activity was detected in ''in vitro'' assays with a functionally active protein {{PubMed|24097949}}
 * '''Protein family:''' UPF0001 family (according to Swiss-Prot)

@@ Line 1: / Line 1: @@
-* '''Description:''' amino acid racemase, production of D-amino acids, control of [[biofilm formation]] <br/><br/>
+* '''Description:''' putative amino acid racemase, production of D-amino acids, control of [[biofilm formation]] <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || amino acid racemase
+|style="background:#ABCDEF;" align="center"| '''Product''' || putative amino acid racemase
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || control of [[biofilm formation]]
@@ Line 58: / Line 58: @@
 === Additional information===
@@ Line 67: / Line 65: @@
 * '''Catalyzed reaction/ biological activity:'''
 * '''Protein family:''' UPF0001 family (according to Swiss-Prot)
@@ Line 76: / Line 75: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''

@@ Line 80: / Line 80: @@
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 136: / Line 137: @@
 =References=
-<pubmed>14651647, 20431016 16420366</pubmed>
+<pubmed>14651647, 20431016 16420366 24097949</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 110: / Line 106: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ylmE_1610170_1610862_1 ylmE] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''

@@ 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=ylmE_1610170_1610862_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ylmE_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ylmE_1610170_1610862_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ylmE_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15380]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylmD]]'', ''[[sepF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15380 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15380 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15380 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15380 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15380 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15380 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ylmE_context.gif]]