CwlT - Revision history

Jstuelk at 16:38, 28 May 2015

2015-05-28T16:38:50Z

Jstuelk at 16:04, 28 May 2015

2015-05-28T16:04:59Z

134.76.38.147 at 13:03, 2 April 2014

2014-04-02T13:03:27Z

Jstuelk at 09:06, 19 February 2014

2014-02-19T09:06:30Z

Jstuelk at 18:17, 18 February 2014

2014-02-18T18:17:27Z

Jstuelk at 18:09, 18 February 2014

2014-02-18T18:09:54Z

Jstuelk: /* References */

2014-02-18T18:01:25Z

‎References

Jstuelk at 10:35, 18 February 2014

2014-02-18T10:35:44Z

134.76.70.252 at 12:37, 16 May 2013

2013-05-16T12:37:46Z

134.76.70.252 at 09:33, 14 May 2013

2013-05-14T09:33:13Z

← Older revision		Revision as of 16:38, 28 May 2015
Line 1:		Line 1:
−	* '''Description:~~''' cell wall hydrolase, required for conjugation of ICE''Bs1'', part of the type IV secretion system for DNA transfer , C-terminal domain hydrolyzes bond between D-Glu and m-DAP <br/><br/>~~	+	{{#bank: CwlT}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''cwlT''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yddH''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\|~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| cell wall hydrolase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| conjugative transfer of ICEBs1~~
−	\|-
−	\|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=BSU04970 cwlT]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 36 kDa, 8.632~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 987 bp, 329 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yddG]]'', ''[[yddI]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU04970 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU04970 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU04970 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yddH_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=yddH_544022_545011_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:cwlT_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU04970]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[mobile genetic elements]]}},~~
−	~~{{SubtiWiki category\|[[cell wall degradation/ turnover]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU04970
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU04970&redirect=T BSU04970]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12115]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** hydrolysis of peptidoglycan (linkage between N-acetylmuramic acid and N-acetylglucosamine and bond between D-γ-glutamate and meso-diaminopimelic acid) {{PubMed\|18305117}}
−	* '''Protein family:''' nlpC/p60 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−	** N-terminal domain is an N-acetylmuramidase that cleaves the linkage between N-acetylmuramic acid and N-acetylglucosamine {{PubMed\|18305117}}
−	** C-terminal endopeptidase domain cleaves the bond between D-γ-glutamate and meso-diaminopimelic acid {{PubMed\|18305117}}
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** secreted (with signal peptide) {{PubMed\|24532767}}
−	** may be a lipoprotein, but the lipid anchor is not required for function {{PubMed\|24532767}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU04970&redirect=T BSU04970]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P96645 P96645]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU04970]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yddH_544022_545011_1 cwlT] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** induced by mitomycin C {{PubMed\|18305117}}
−
−	* '''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>,18305117, 24532767 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 1: / Line 1: @@
-* '''Description:''' cell wall hydrolase, required for conjugation of ICE''Bs1'', C-terminal domain hydrolyzes bond between D-Glu and m-DAP <br/><br/>
+* '''Description:''' cell wall hydrolase, required for conjugation of ICE''Bs1'', part of the type IV secretion system for DNA transfer , C-terminal domain hydrolyzes bond between D-Glu and m-DAP <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || cell wall hydrolase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || conjugation of ICE''Bs1''
+|style="background:#ABCDEF;" align="center"|'''Function''' || conjugative transfer of ICEBs1
 |-
 |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=BSU04970 cwlT]

@@ Line 53: / Line 53: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 91: / Line 92: @@
 === Database entries ===
 * '''Structure:'''

← Older revision		Revision as of 09:06, 19 February 2014
Line 38:		Line 38:

	= [[Categories]] containing this gene/protein =		= [[Categories]] containing this gene/protein =
		+	{{SubtiWiki category\|[[mobile genetic elements]]}},
	{{SubtiWiki category\|[[cell wall degradation/ turnover]]}}		{{SubtiWiki category\|[[cell wall degradation/ turnover]]}}

@@ Line 1: / Line 1: @@
-* '''Description:''' cell wall hydrolase, C-terminal domain hydrolyzes bond between D-Glu and m-DAP <br/><br/>
+* '''Description:''' cell wall hydrolase, required for conjugation of ICE''Bs1'', C-terminal domain hydrolyzes bond between D-Glu and m-DAP <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || cell wall hydrolase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall metabolism
+|style="background:#ABCDEF;" align="center"|'''Function''' || conjugation of ICE''Bs1''
 |-
 |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=BSU04970 cwlT]
@@ Line 64: / Line 64: @@
 * '''Catalyzed reaction/ biological activity:'''
+** hydrolysis of peptidoglycan (linkage between N-acetylmuramic acid and N-acetylglucosamine and bond between D-γ-glutamate and  meso-diaminopimelic acid) {{PubMed|18305117}}
 * '''Protein family:''' nlpC/p60 family (according to Swiss-Prot)
@@ Line 74: / Line 74: @@
 * '''[[Domains]]:'''
-** N-terminal domain is an N-acetylmuramidase that cleaves the linkage between N-acetylmuramic acid and N-acetylglucosamine {{PubMed|22383849}}
+** N-terminal domain is an N-acetylmuramidase that cleaves the linkage between N-acetylmuramic acid and N-acetylglucosamine {{PubMed|18305117}}
-** C-terminal endopeptidase domain cleaves the bond between D-γ-glutamate and  meso-diaminopimelic acid
+** C-terminal endopeptidase domain cleaves the bond between D-γ-glutamate and  meso-diaminopimelic acid {{PubMed|18305117}}
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 86: / Line 86: @@
 * '''[[Localization]]:'''
 === Database entries ===
@@ Line 105: / Line 107: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yddH_544022_545011_1 cwlT] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 62: / Line 58: @@
 === Additional information===
 =The protein=
@@ Line 80: / Line 73: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''

@@ Line 139: / Line 139: @@
 =References=
-<pubmed>,18305117, </pubmed>
+<pubmed>,18305117, 24532767 </pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 10:35, 18 February 2014
Line 1:		Line 1:
−		+	* '''Description:''' cell wall hydrolase, C-terminal domain hydrolyzes bond between D-Glu and m-DAP <br/><br/>

	{\| align="right" border="1" cellpadding="2"		{\| align="right" border="1" cellpadding="2"

@@ 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=yddH_544022_545011_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cwlT_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yddH_544022_545011_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:cwlT_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU04970]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yddG]]'', ''[[yddI]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU04970 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU04970 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU04970 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU04970 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU04970 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU04970 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yddH_context.gif]]