NagR - Revision history

Jstuelk: /* References */

2015-07-13T07:59:38Z

‎References

Jstuelk at 16:41, 16 February 2015

2015-02-16T16:41:51Z

Jstuelk: /* References */

2015-01-08T10:27:50Z

‎References

Jstuelk at 10:12, 8 January 2015

2015-01-08T10:12:43Z

Fabian Commichau: /* References */

2015-01-08T10:06:51Z

‎References

134.76.38.147 at 14:54, 2 April 2014

2014-04-02T14:54:04Z

Jstuelk: /* Expression and regulation */

2014-03-31T10:50:39Z

‎Expression and regulation

Jstuelk: /* Basic information/ Evolution */

2014-03-31T10:49:53Z

‎Basic information/ Evolution

Jstuelk at 07:40, 31 March 2014

2014-03-31T07:40:14Z

134.76.70.252 at 11:46, 7 January 2014

2014-01-07T11:46:01Z

← Older revision		Revision as of 07:59, 13 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' transcriptional regulator ([[GntR family]]) <br/><br/>~~	+	{{#bank: NagR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''nagR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yvoA ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| transcriptional regulator ([[GntR family]])~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| probably regulator of the putative ''[[nagA]]-[[nagB]]-[[yvoA]]'' operon~~
−	\|-
−	\|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=BSU35030 nagR]
−	\|-
−	\|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=nagR nagR]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 27 kDa, 6.768~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 729 bp, 243 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[nagB]]'', ''[[yvnB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35030 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35030 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35030 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yvoA_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=yvoA_3597289_3598020_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:nagR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35030]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[utilization of specific carbon sources]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[NagR regulon]]}}~~
−	~~=The [[NagR regulon]]:=~~
−	* ''[[nagA]]-[[nagB]]-[[nagR]]'', ''[[nagP]]''
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU35030
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35030&redirect=T BSU35030]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14124]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' transcription repression of ''[[nagP]]'' and of the putative ''[[nagA]]-[[nagB]]-[[nagR]]'' operon in the absence of N-acetylglycosamine {{PubMed\|24673833,20047956,21602348}}, weak repression of ''[[yflG]]'' {{PubMed\|16207374}}
−
−	* '''Protein family:''' [[GntR family]] of transcription factors
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:''' K(D) for N-acetylglucosamine-6-phosphate: 1 mM {{PubMed\|20047956}}
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−	** N-acetylglucosamine-6-phosphate and glucosamine-6-phosphate act as the molecular inducers {{PubMed\|25564531,21602348,20047956}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35030&redirect=T BSU35030]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/search/structidSearch.do?structureId=2WV0 2WVO] {{PubMed\|20047956}}
−	** [http://www.rcsb.org/pdb/explore/explore.do?structureId=4wwc 4WWC] (complex with palindromic operator DNA) {{PubMed\|25564531}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34817 O34817]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35030]
−
−	* '''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=yvoA_3597289_3598020_1 nagR] {{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}}
−
−	* '''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>19342794,20047956 16207374 21602348 23667565 24673833 25564531 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 96: / Line 96: @@
 * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35030&redirect=T BSU35030]
-* '''Structure:''' [http://www.rcsb.org/pdb/search/structidSearch.do?structureId=2WV0 2WVO] {{PubMed|20047956}}
+* '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O34817 O34817]

@@ Line 140: / Line 140: @@
 =References=
-<pubmed>19342794,20047956 16207374 21602348 23667565 24673833 25564531 25564531 </pubmed>
+<pubmed>19342794,20047956 16207374 21602348 23667565 24673833 25564531 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 87: / Line 87: @@
 * '''Effectors of protein activity:'''
-** N-acetylglucosamine-6-phosphate acts as the molecular inducer {{PubMed|20047956}}
+** N-acetylglucosamine-6-phosphate and glucosamine-6-phosphate act as the molecular inducers {{PubMed|25564531,21602348,20047956}}
 * '''[[SubtInteract|Interactions]]:'''
@@ Line 141: / Line 140: @@
 =References=
-<pubmed>19342794,20047956 16207374 21602348 23667565 24673833 25564531 </pubmed>
+<pubmed>19342794,20047956 16207374 21602348 23667565 24673833 25564531 25564531 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 141: / Line 141: @@
 =References=
-<pubmed>19342794,20047956 16207374 21602348 23667565 24673833 </pubmed>
+<pubmed>19342794,20047956 16207374 21602348 23667565 24673833 25564531 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 94: / Line 95: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/search/structidSearch.do?structureId=2WV0 2WVO] {{PubMed|20047956}}

@@ Line 113: / Line 113: @@
 * '''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}}
 * '''Additional information:'''

@@ Line 69: / Line 69: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:''' transcription repression of ''[[nagP]]'' and of the putative ''[[nagA]]-[[nagB]]-[[nagR]]'' operon in the absence of N-acetylglycosamine {{PubMed|20047956,21602348}}, weak repression of ''[[yflG]]'' {{PubMed|16207374}}
+* '''Catalyzed reaction/ biological activity:''' transcription repression of ''[[nagP]]'' and of the putative ''[[nagA]]-[[nagB]]-[[nagR]]'' operon in the absence of N-acetylglycosamine {{PubMed|24673833,20047956,21602348}}, weak repression of ''[[yflG]]'' {{PubMed|16207374}}
 * '''Protein family:''' [[GntR family]] of transcription factors

@@ Line 71: / Line 71: @@
 * '''Catalyzed reaction/ biological activity:''' transcription repression of ''[[nagP]]'' and of the putative ''[[nagA]]-[[nagB]]-[[nagR]]'' operon in the absence of N-acetylglycosamine {{PubMed|20047956,21602348}}, weak repression of ''[[yflG]]'' {{PubMed|16207374}}
-* '''Protein family:'''
+* '''Protein family:''' [[GntR family]] of transcription factors
 * '''Paralogous protein(s):'''
@@ Line 79: / Line 79: @@
 * '''Kinetic information:''' K(D) for N-acetylglucosamine-6-phosphate: 1 mM {{PubMed|20047956}}
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 139: / Line 139: @@
 =References=
-<pubmed>19342794,20047956 16207374 21602348 23667565</pubmed>
+<pubmed>19342794,20047956 16207374 21602348 23667565 24673833 </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=BSU35030 nagR]
 |-
-|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=nagR nagR]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 6.768