NagZ - Revision history

Julian at 12:54, 24 April 2014

2014-04-24T12:54:32Z

Julian at 11:06, 24 April 2014

2014-04-24T11:06:41Z

Julian at 08:53, 22 April 2014

2014-04-22T08:53:39Z

134.76.38.147 at 12:51, 2 April 2014

2014-04-02T12:51:34Z

134.76.70.252 at 10:02, 7 January 2014

2014-01-07T10:02:36Z

Raphael2215: /* Database entries */

2013-07-10T08:43:02Z

‎Database entries

134.76.70.252 at 12:24, 16 May 2013

2013-05-16T12:24:49Z

134.76.70.252 at 09:19, 14 May 2013

2013-05-14T09:19:07Z

134.76.70.252 at 12:00, 13 May 2013

2013-05-13T12:00:25Z

Jstuelk: /* References */

2012-11-28T14:51:26Z

‎References

← Older revision		Revision as of 12:54, 24 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' N-acetylglucosaminidase <br/><br/>~~	+	{{#bank: NagZ}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''nagZ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yzbA, ybbD ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| N-acetylglucosaminidase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| cell wall recycling~~
−	\|-
−	\|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=BSU01660 nagZ]
−	\|-
−	\|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=nagZ nagZ]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 70 kDa, 9.76~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1926 bp, 642 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ybbC]]'', ''[[amiE]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01660 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01660 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01660 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ybbD_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=ybbD_186452_188380_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:nagZ_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01660]]
−	\|-
−	\|}
−
−	~~__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]]}},~~
−	~~{{SubtiWiki category\|[[Sporulation#Sporulation_proteins/_other\|sporulation proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU01660
−
−	~~===Phenotypes of a mutant ===~~
−	~~increased autolysis {{PubMed\|20400549}}~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01660&redirect=T BSU01660]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10832]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' cleaves muropeptides derived from peptidoglycan, but not peptidoglycan itself {{PubMed\|20400549}}
−
−	* '''Protein family:''' glycosyl hydrolase 3 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** secreted (with signal peptide), remains to some extent cell wall-associated {{PubMed\|20400549}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01660&redirect=T BSU01660]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3BMX 3BMX] {{PubMed\|20826810}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P40406 P40406]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01660]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.52 3.2.1.52]
−
−	~~=== Additional information===~~
−	The gene is mis-annotated in KEGG as an ortholog of beta-N-acetylhexosaminidase EC 3.2.1.52. It is marked in MetaCyc as “similar to beta-hexosaminidase”. No EC annotation is available in Swiss-ProtSwiss-Prot.supporting the annotation is available. {{PubMed\|19935659}}
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[murQ]]-[[murR]]-[[murP]]-[[amiE]]-[[nagZ]]-[[ybbC]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbD_186452_188380_-1 nagZ] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** expressed in late exponential and early stationary phase {{PubMed\|20400549}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' available in [[Christoph Mayer]]'s lab {{PubMed\|20400549}}
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~'''Additional references:''' {{PubMed\|23177201,20826810}}~~
−	~~<pubmed>10627040, 20400549 4628806 4196675 22383849</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 41: / Line 41: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[cell wall degradation/ turnover]]}},
-{{SubtiWiki category|[[sporulation/ other]]}}
+{{SubtiWiki category|[[Sporulation#Sporulation_proteins/_other|sporulation proteins]]}}
 = This gene is a member of the following [[regulons]] =

@@ Line 40: / Line 40: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[cell wall degradation/ turnover]]}}
+{{SubtiWiki category|[[cell wall degradation/ turnover]]}},
 = This gene is a member of the following [[regulons]] =

@@ Line 55: / Line 55: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3BMX 3BMX] {{PubMed|20826810}}

@@ Line 16: / Line 16: @@
 |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=BSU01660 nagZ]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/murein/index.html Murein recycling]'''
+|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=nagZ nagZ]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 70 kDa, 9.76

@@ Line 94: / Line 94: @@
 === Database entries ===
-* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3CQM 3CQM] {{PubMed|20826810}}
+* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3BMX 3BMX] {{PubMed|20826810}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P40406 P40406]

@@ Line 29: / Line 29: @@
   <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=ybbD_186452_188380_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:nagZ_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ybbD_186452_188380_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:nagZ_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01660]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybbC]]'', ''[[amiE]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01660 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01660 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01660 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01660 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01660 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01660 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ybbD_context.gif]]

@@ Line 139: / Line 139: @@
 =References=
-'''Additional references:''' {{PubMed|20826810}}
+'''Additional references:''' {{PubMed|23177201,20826810}}
-<pubmed>10627040, 20400549 4628806 4196675 22383849 23177201</pubmed>
+<pubmed>10627040, 20400549 4628806 4196675 22383849</pubmed>
 [[Category:Protein-coding genes]]