NagB - Revision history

Jstuelk: /* References */

2015-07-13T08:00:20Z

‎References

Fabian Commichau: /* References */

2015-01-08T10:07:42Z

‎References

134.76.38.147 at 14:53, 2 April 2014

2014-04-02T14:53:56Z

Jstuelk at 10:51, 31 March 2014

2014-03-31T10:51:57Z

134.76.70.252 at 11:45, 7 January 2014

2014-01-07T11:45:58Z

Jstuelk: /* References */

2013-07-25T10:48:35Z

‎References

Jstuelk at 16:42, 24 May 2013

2013-05-24T16:42:03Z

134.76.70.252 at 14:40, 16 May 2013

2013-05-16T14:40:57Z

134.76.70.252 at 11:22, 14 May 2013

2013-05-14T11:22:59Z

134.76.70.252 at 13:57, 13 May 2013

2013-05-13T13:57:37Z

← Older revision		Revision as of 08:00, 13 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' glucosamine-6-phosphate deaminase <br/><br/>~~	+	{{#bank: NagB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''nagB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| glucosamine-6-phosphate deaminase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| N-acetylglucosamine utilization~~
−	\|-
−	\|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=BSU35020 nagB]
−	\|-
−	\|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=nagB nagB]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 26 kDa, 5.717~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 726 bp, 242 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[nagA]]'', ''[[nagR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35020 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35020 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35020 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:nagB_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=nagBA_3596543_3597271_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:nagB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35020]]
−	\|-
−	\|}
−
−	~~__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\|[[utilization of specific carbon sources]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[NagR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU35020
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35020&redirect=T BSU35020]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12631]
−
−	~~=== Additional information===~~
−	* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed\|21821766}}
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' D-glucosamine 6-phosphate + H<sub>2</sub>O = D-fructose 6-phosphate + NH<sub>3</sub> (according to Swiss-Prot)
−
−	* '''Protein family:''' NagB subfamily (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[GamA]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35020&redirect=T BSU35020]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2BKX 2BKX]{{PubMed\|15755726}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O35000 O35000]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35020]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[nagA]]-[[nagB]]-[[nagR]]'' {{PubMed\|21602348}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nagBA_3596543_3597271_1 nagB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|23667565}}
−
−	* '''Regulation:'''
−	** induced in the presence of N-acetylglucosamine ([[NagR]]) {{PubMed\|24673833,21602348}}
−
−	* '''Regulatory mechanism:'''
−	** [[NagR]]: transcription repression {{PubMed\|24673833,21602348}}
−
−	* '''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>6174502,15755726 21821766 21602348 23667565 24673833,23876412 25564531 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 139: / Line 139: @@
 =References=
-<pubmed>6174502,15755726 21821766 21602348 23667565 24673833,23876412</pubmed>
+<pubmed>6174502,15755726 21821766 21602348 23667565 24673833,23876412 25564531 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 55: / Line 55: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 90: / Line 91: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2BKX 2BKX]{{PubMed|15755726}}

@@ Line 77: / Line 77: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 109: / Line 109: @@
 * '''Regulation:'''
-** induced in the presence of N-acetylglucosamine ([[NagR]]) {{PubMed|21602348}}
+** induced in the presence of N-acetylglucosamine ([[NagR]]) {{PubMed|24673833,21602348}}
 * '''Regulatory mechanism:'''
-** [[NagR]]: transcription repression {{PubMed|21602348}}
+** [[NagR]]: transcription repression {{PubMed|24673833,21602348}}
 * '''Regulatory mechanism:'''
@@ Line 137: / Line 137: @@
 =References=
-<pubmed>6174502,15755726 21821766 21602348 23667565 23876412</pubmed>
+<pubmed>6174502,15755726 21821766 21602348 23667565 24673833,23876412</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=BSU35020 nagB]
 |-
-|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/carbohydrate_metabolic_pathways.html Sugar catabolism], [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=nagB nagB]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 5.717

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 110: / Line 106: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nagBA_3596543_3597271_1 nagB] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|23667565}}
 * '''Regulation:'''
@@ Line 141: / Line 137: @@
 =References=
-'''Additional publications:''' {{PubMed|21602348}}
+<pubmed>6174502,15755726 21821766 21602348 23667565</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=nagBA_3596543_3597271_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:nagB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nagBA_3596543_3597271_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:nagB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35020]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nagA]]'', ''[[nagR]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35020 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35020 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35020 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35020 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35020 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35020 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:nagB_context.gif]]