GabR - Revision history

Jstuelk: /* References */

2015-04-26T15:41:35Z

‎References

Fabian Commichau: /* References */

2014-11-14T06:11:28Z

‎References

134.76.38.147 at 12:59, 2 April 2014

2014-04-02T12:59:35Z

Jstuelk at 19:44, 21 December 2013

2013-12-21T19:44:23Z

Jstuelk: /* The protein */

2013-12-21T19:36:10Z

‎The protein

Jstuelk: /* Basic information/ Evolution */

2013-11-22T13:36:11Z

‎Basic information/ Evolution

Fabian Commichau: /* References */

2013-11-22T08:16:51Z

‎References

Fabian Commichau at 07:57, 22 November 2013

2013-11-22T07:57:58Z

Fabian Commichau: /* Labs working on this gene/protein */

2013-11-22T07:46:59Z

‎Labs working on this gene/protein

Fabian Commichau: /* Basic information/ Evolution */

2013-11-21T16:07:38Z

‎Basic information/ Evolution

← Older revision		Revision as of 15:41, 26 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' transcription activator of ''[[gabT]]-[[gabD]]'', repressor of ''gabR'' ([[MocR/~~ GabR ~~family]]) <br/><br/>~~	+	{{#bank: GabR}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''gabR''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ycnF ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| transcription regulator~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of gamma-amino butyric acid 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=BSU03890 gabR]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 54 kDa, 6.709~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1437 bp, 479 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yczG]]'', ''[[gabT]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU03890 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU03890 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU03890 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:gabR_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=gabR_440025_441464_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:gabR_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU03890]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[utilization of amino acids]]}},~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[GabR regulon]]}}~~
−	~~=The [[GabR regulon]]:=~~
−	* ''[[gabT]]-[[gabD]]'', ''[[gabR]]''
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU03890
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU03890&redirect=T BSU03890]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gabR.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12042]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** transcription activation of the ''[[gabT]]-[[gabD]]'' operon in the presence of GABA and PLP, transcription repression of ''[[gabR]]'' {{PubMed\|15223311}}
−
−	* '''Protein family:''' [[MocR/ GabR family]] [http://www.ncbi.nlm.nih.gov/sites/entrez/22020104 PubMed]
−
−	* '''Paralogous protein(s):''' none, but there are 7 members of the [[MocR/ GabR family]] in ''B. subtilis''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−	** N-terminal DNA-binding helix-turn-helix motif (corresponding to domains of the [[GntR family]]) {{PubMed\|24127574}}
−	** C-terminal domain is homologous to PLP-binding large domain of aminotransferases {{PubMed\|24127574}}
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:''' gamma-aminobutyric acid, PLP {{PubMed\|24127574}}
−
−	* '''Effectors of protein activity:'''
−	** activation of ''[[gabT]]-[[gabD]]'' expression is triggered by gamma-amino butyrate and pyridoxalphosphate {{PubMed\|15223311}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** forms head-to-tail domain-swapped dimers {{PubMed\|24127574}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU03890&redirect=T BSU03890]
−
−	* '''Structure:'''
−	** [http://www.rcsb.org/pdb/explore/explore.do?structureId=4MGR 4MGR] (the apo-protein) {{PubMed\|24127574}}
−	** [http://www.rcsb.org/pdb/explore/explore.do?structureId=4N0B 4N0B] (the complex with PLP) {{PubMed\|24127574}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P94426 P94426]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU03890]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[gabR]]'' (according to [http://dbtbs.hgc.jp/COG/prom/gabR.html DBTBS])
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gabR_440025_441464_-1 gabR] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|12123465}}
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** GabR: negative autoregulation {{PubMed\|12123465}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Linc Sonenshein\|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed> 11756427 15223311,12123465, 24127574 22020104 25388514 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 145: / Line 145: @@
 =References=
-<pubmed> 11756427 15223311,12123465, 24127574 22020104 </pubmed>
+<pubmed> 11756427 15223311,12123465, 24127574 22020104 25388514 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gabR.html]
@@ Line 93: / Line 94: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 66: / Line 66: @@
 * '''Catalyzed reaction/ biological activity:'''
-** transcription activation of the ''[[gabT]]-[[gabD]]'' operon, transcription repression of ''[[gabR]]'' {{PubMed|15223311}}
+** transcription activation of the ''[[gabT]]-[[gabD]]'' operon in the presence  of GABA and PLP, transcription repression of ''[[gabR]]'' {{PubMed|15223311}}
 * '''Protein family:''' [[MocR/ GabR family]] [http://www.ncbi.nlm.nih.gov/sites/entrez/22020104 PubMed]
@@ Line 88: / Line 88: @@
 * '''[[SubtInteract|Interactions]]:'''
 * '''[[Localization]]:'''

@@ Line 76: / Line 76: @@
 * '''Kinetic information:'''
-* '''Domains:''' N-terminal DNA-binding helix-turn-helix motif; C-terminal domain is homologous to PLP-binding large domain of aminotransferases.
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:''' gamma-aminobutyric acid, PLP {{PubMed|24127574}}
 * '''Effectors of protein activity:'''
@@ Line 91: / Line 93: @@
 === Database entries ===
-* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=4MGR 4MGR] {{PubMed|24127574}}
+* '''Structure:'''
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P94426 P94426]

@@ Line 68: / Line 68: @@
 ** transcription activation of the ''[[gabT]]-[[gabD]]'' operon, transcription repression of ''[[gabR]]'' {{PubMed|15223311}}
-* '''Protein family:''' MocR/ GabR family [http://www.ncbi.nlm.nih.gov/sites/entrez/22020104 PubMed]
+* '''Protein family:''' [[MocR/ GabR family]] [http://www.ncbi.nlm.nih.gov/sites/entrez/22020104 PubMed]
-* '''Paralogous protein(s):''' none, but there are 7 members of the MocR/ GabR family in ''B. subtilis''
+* '''Paralogous protein(s):''' none, but there are 7 members of the [[MocR/ GabR family]] in ''B. subtilis''
 === Extended information on the protein ===

← Older revision		Revision as of 07:57, 22 November 2013
Line 1:		Line 1:
−	* '''Description:''' transcription activator of ''[[gabT]]-[[gabD]]'', repressor of ''gabR'' (MocR/ GabR family) <br/><br/>	+	* '''Description:''' transcription activator of ''[[gabT]]-[[gabD]]'', repressor of ''gabR'' ([[MocR/ GabR family]]) <br/><br/>

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

← Older revision		Revision as of 07:46, 22 November 2013
Line 131:		Line 131:

	=Labs working on this gene/protein=		=Labs working on this gene/protein=
		+
		+	[[Linc Sonenshein\|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

	=Your additional remarks=		=Your additional remarks=