GamA - Revision history

134.76.70.252 at 10:08, 17 April 2014

2014-04-17T10:08:09Z

134.76.38.147 at 12:54, 2 April 2014

2014-04-02T12:54:01Z

Jstuelk at 10:52, 31 March 2014

2014-03-31T10:52:48Z

Jstuelk at 07:41, 31 March 2014

2014-03-31T07:41:38Z

Jstuelk at 17:14, 27 February 2014

2014-02-27T17:14:18Z

134.76.70.252 at 10:04, 7 January 2014

2014-01-07T10:04:45Z

Jstuelk: /* References */

2013-07-25T10:48:56Z

‎References

Jstuelk at 16:58, 24 May 2013

2013-05-24T16:58:57Z

Jstuelk: /* This gene is a member of the following regulons */

2013-05-24T16:25:22Z

‎This gene is a member of the following regulons

Jstuelk at 16:25, 24 May 2013

2013-05-24T16:25:00Z

← Older revision		Revision as of 10:08, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' glucosamine-6-phosphate deaminase <br/><br/>~~	+	{{#bank: GamA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''gamA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ybfT ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| glucosamine-6-phosphate deaminase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| glucosamine 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=BSU02360 gamA]
−	\|-
−	\|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=gamA gamA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 27 kDa, 5.793~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 747 bp, 249 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[gamP]]'', ''[[gamR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02360 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02360 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02360 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:gamA_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=nagBB_256823_257572_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:gamA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02360]]
−	\|-
−	\|}
−
−	~~__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\|[[GamR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU02360
−
−	~~===Phenotypes of a mutant ===~~
−	* no growth on glucosamine {{PubMed\|23667565}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU02360&redirect=T BSU02360]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12746]
−
−	~~=== Additional information===~~
−
−	~~=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):''' [[NagB]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:''' K(M): 3.0 mM {{PubMed\|14343123}}
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU02360&redirect=T BSU02360]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=2bkx 2BKX] (the structure of [[NagB]], 50% identity) {{PubMed\|15755726}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O31458 O31458]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU02360]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[gamA]]-[[gamP]]'' {{PubMed\|23667565}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nagBB_256823_257572_-1 gamA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|23667565}}
−
−	* '''Regulation:'''
−	** induced by N-acetylglucosamine {{PubMed\|14343123}}
−	** induced by glucosamine ([[GamR]]) {{PubMed\|24673833,23667565}}
−
−	* '''Regulatory mechanism:'''
−	** [[GamR]]: transcription repression {{PubMed\|24673833,23667565}}
−
−	* '''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>10627040, 14343123 23667565 23876412 24673833,15755726 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 90: / Line 91: @@
 === Database entries ===
 * '''Structure:'''	[http://www.pdb.org/pdb/explore/explore.do?structureId=2bkx 2BKX] (the structure of [[NagB]], 50% identity) {{PubMed|15755726}}

@@ Line 111: / Line 111: @@
 * '''Regulation:'''
 ** induced by N-acetylglucosamine {{PubMed|14343123}}
-** induced by glucosamine ([[GamR]]) {{PubMed|23667565}}
+** induced by glucosamine ([[GamR]]) {{PubMed|24673833,23667565}}
 * '''Regulatory mechanism:'''
-** [[GamR]]: transcription repression {{PubMed|23667565}}
+** [[GamR]]: transcription repression {{PubMed|24673833,23667565}}
 * '''Additional information:'''
@@ Line 138: / Line 138: @@
 =References=
-<pubmed>10627040, 14343123 23667565 23876412 15755726 </pubmed>
+<pubmed>10627040, 14343123 23667565 23876412 24673833,15755726 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 747 bp, 249 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gamP]]'', ''[[ybgA]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gamP]]'', ''[[gamR]]''
 |-
 |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02360 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02360 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02360 DNA_with_flanks]
@@ Line 44: / Line 44: @@
 = This gene is a member of the following [[regulons]] =
-{{SubtiWiki regulon|[[YbgA regulon]]}}
+{{SubtiWiki regulon|[[GamR regulon]]}}
 =The gene=
@@ Line 111: / Line 111: @@
 * '''Regulation:'''
 ** induced by N-acetylglucosamine {{PubMed|14343123}}
-** induced by glucosamine ([[YbgA]]) {{PubMed|23667565}}
+** induced by glucosamine ([[GamR]]) {{PubMed|23667565}}
 * '''Regulatory mechanism:'''
-** [[YbgA]]: transcription repression {{PubMed|23667565}}
+** [[GamR]]: transcription repression {{PubMed|23667565}}
 * '''Additional information:'''

@@ Line 62: / Line 62: @@
 === Additional information===
 =The protein=
@@ Line 80: / Line 77: @@
 * '''Kinetic information:''' K(M): 3.0 mM {{PubMed|14343123}}
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
@@ Line 94: / Line 91: @@
 === Database entries ===
-* '''Structure:'''
+* '''Structure:'''	[http://www.pdb.org/pdb/explore/explore.do?structureId=2bkx 2BKX] (the structure of [[NagB]], 50% identity) {{PubMed|15755726}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/O31458 O31458]
@@ Line 141: / Line 138: @@
 =References=
-<pubmed>10627040, 14343123 23667565 23876412</pubmed>
+<pubmed>10627040, 14343123 23667565 23876412 15755726 </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=BSU02360 gamA]
 |-
-|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]'''
+|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=gamA gamA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 5.793

@@ Line 106: / Line 106: @@
 =Expression and regulation=
-* '''Operon:''' ''[[gamA]]-[[gamP]]''
+* '''Operon:''' ''[[gamA]]-[[gamP]]'' {{PubMed|23667565}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=nagBB_256823_257572_-1 gamA] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|23667565}}
 * '''Regulation:'''
 ** induced by N-acetylglucosamine {{PubMed|14343123}}
 * '''Regulatory mechanism:'''
 * '''Additional information:'''

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 48: / Line 44: @@
 = This gene is a member of the following [[regulons]] =
@@ Line 57: / Line 54: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 142: / Line 140: @@
 =References=
-<pubmed>10627040, 14343123 </pubmed>
+<pubmed>10627040, 14343123 23667565</pubmed>
 [[Category:Protein-coding genes]]