LytF - Revision history

Jstuelk at 13:08, 9 October 2014

2014-10-09T13:08:15Z

Jstuelk at 14:23, 18 May 2014

2014-05-18T14:23:44Z

134.76.70.252 at 11:49, 8 April 2014

2014-04-08T11:49:20Z

134.76.38.147 at 13:17, 2 April 2014

2014-04-02T13:17:20Z

Jstuelk: /* Extended information on the protein */

2013-12-27T14:50:09Z

‎Extended information on the protein

Jstuelk at 14:46, 27 December 2013

2013-12-27T14:46:23Z

134.76.70.252 at 15:31, 11 November 2013

2013-11-11T15:31:23Z

Jstuelk at 16:51, 19 July 2013

2013-07-19T16:51:44Z

Jstuelk at 12:34, 16 July 2013

2013-07-16T12:34:13Z

134.76.70.252 at 12:51, 16 May 2013

2013-05-16T12:51:48Z

← Older revision		Revision as of 13:08, 9 October 2014
Line 1:		Line 1:
−	* '''Description:''' gamma-D-glutamate-meso-diaminopimelate muropeptidase, cell separase (major autolysin) <br/><br/>	+	{{#bank: LytF}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:~~#~~ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''lytF''~~
−	\|-
−	~~\|style="background~~:~~#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''cwlE, yhdD ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| gamma-D-glutamate-meso-diaminopimelate muropeptidase (major autolysin)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| cell separation~~
−	\|-
−	\|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=BSU09370 lytF]
−	\|-
−	\|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=LytF ~~LytF]~~
−	\|-
−	\|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=LytF LytF]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 51 kDa, 10.41~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1464 bp, 488 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yhdC]]'', ''[[nsrR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09370 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09370 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09370 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:lytF_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=lytF_1011792_1013258_-1 Expression at a glance]'''   {{PubMed\|22383849}~~}~~<br/>[[Image:lytF_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09370]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[cell wall degradation/ turnover]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigD regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SlrR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU09370
−
−	~~===Phenotypes of a mutant ===~~
−	* cell separation defect, this is increased by a ''[[lytE]]'' mutation {{PubMed\|23855774}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09370&redirect=T BSU09370]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lytF.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13010]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' nlpC/p60 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' the C-terminal D,L-endopeptidase domains of [[LytE]], [[LytF]], [[CwlS]], and [[CwlO]] exhibit strong sequence similarity
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−	** contains five N-acetylglucosamine-polymer-binding [[LysM domain]]s {{PubMed\|18430080}}
−	** C-terminal D,L-endopeptidase domain {{PubMed\|22139507}}
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[IseA]]-[[LytF]] (catalytic domain) {{PubMed\|18761696}}
−
−	* '''[[Localization]]:'''
−	**secreted (according to Swiss-Prot)
−	** localizes to cell septa and poles {{PubMed\|22139507}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09370&redirect=T BSU09370]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O07532 O07532]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09370]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[lytF]]'' {{PubMed\|10322020}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lytF_1011792_1013258_-1 lytF] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigD]] {{PubMed\|10322020}}
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** [[SlrR]] (in complex with [[SinR]]: transcription repression {{PubMed\|20351052}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A791 ( ''lytF''::''spec''), {{PubMed\|10206711}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A791&Search=1A791 BGSC]
−	** 1A792 ( ''lytF''::''spec''), {{PubMed\|1588906}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A792&Search=1A792 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~== Reviews==~~
−	~~<pubmed>18430080</pubmed>~~
−	~~== Original publications ==~~
−	~~<pubmed> 20351052,10322020,10206711,14594841,18761696, 19542270 22139507 23855774 23091053</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 1: / Line 1: @@
-* '''Description:''' gamma-D-glutamate-meso-diaminopimelate muropeptidase (major autolysin) <br/><br/>
+* '''Description:''' gamma-D-glutamate-meso-diaminopimelate muropeptidase, cell separase (major autolysin) <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-

@@ Line 16: / Line 16: @@
 |-
 |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=LytF LytF]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 10.41

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lytF.html]
@@ Line 97: / Line 98: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 80: / Line 80: @@
 * '''[[Domains]]:'''
-** contains four N-acetylglucosamine-polymer-binding [[LysM domain]]s {{PubMed|18430080}}
+** contains five N-acetylglucosamine-polymer-binding [[LysM domain]]s {{PubMed|18430080}}
 ** C-terminal D,L-endopeptidase domain {{PubMed|22139507}}

@@ Line 79: / Line 79: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 ** C-terminal D,L-endopeptidase domain {{PubMed|22139507}}
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 143: / Line 144: @@
 =References=
 <pubmed> 20351052,10322020,10206711,14594841,18761696, 19542270 22139507 23855774 23091053</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=BSU09370 lytF]
 |-
-|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/LytF LytF]
+|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=LytF LytF]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 51 kDa, 10.41

@@ Line 54: / Line 54: @@
 ===Phenotypes of a mutant ===
-*  cell separation defect, this is increased  by a ''[[lytE]]'' mutation {{PubMed|xxx}}
+*  cell separation defect, this is increased  by a ''[[lytE]]'' mutation {{PubMed|23855774}}
 === Database entries ===
@@ Line 143: / Line 143: @@
 =References=
-'''Additional publications:''' {{PubMed|23091053}}
+<pubmed> 20351052,10322020,10206711,14594841,18761696, 19542270 22139507 23855774 23091053</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 54: / Line 54: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 112: / Line 113: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lytF_1011792_1013258_-1 lytF] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigD]] {{PubMed|10322020}}
+* '''[[Sigma factor]]:''' [[SigD]] {{PubMed|10322020}}
 * '''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=lytF_1011792_1013258_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:lytF_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lytF_1011792_1013258_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:lytF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09370]]
 |-
 |}