GabP - Revision history

Jstuelk: /* References */

2015-07-30T08:21:23Z

‎References

134.76.70.252 at 09:58, 17 April 2014

2014-04-17T09:58:40Z

134.76.38.147 at 13:07, 2 April 2014

2014-04-02T13:07:38Z

134.76.70.252 at 10:16, 7 January 2014

2014-01-07T10:16:38Z

Jstuelk: /* Basic information/ Evolution */

2013-11-28T18:42:08Z

‎Basic information/ Evolution

Jstuelk: /* The protein */

2013-11-28T12:48:42Z

‎The protein

Jstuelk: /* The protein */

2013-11-28T12:45:23Z

‎The protein

Jstuelk at 12:34, 28 November 2013

2013-11-28T12:34:47Z

Jstuelk: /* Basic information/ Evolution */

2013-11-28T12:32:41Z

‎Basic information/ Evolution

Jstuelk: /* Biological materials */

2013-11-28T12:20:52Z

‎Biological materials

← Older revision		Revision as of 08:21, 30 July 2015
Line 1:		Line 1:
−	* '''Description:''' gamma-amino butyric acid permease and minor proline permease<br/><br/>	+	{{#bank: GabP}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''gabP''~~
−	\|-
−	~~\|style="background:~~#~~ABCDEF;" align="center"\| '''Synonyms''' \|\| ''nrg-21 ''~~
−	\|-
−	~~\|style="background~~:~~#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| gamma-amino butyric acid permease~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| utilization of gamma-amino butyric acid~~
−	\|-
−	\|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=BSU06310 gabP]
−	\|-
−	\|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=gabP gabP]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 50 kDa, 9.45~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1407 bp, 469 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[cotA]]'', ''[[ydzX]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU06310 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU06310 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU06310 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:gabP_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=gabP_685155_686564_-1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:gabP_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU06310]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transporters/ other]]}},~~
−	~~{{SubtiWiki category\|[[utilization of amino acids]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[TnrA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU06310
−
−	~~===Phenotypes of a mutant ===~~
−	* defective in the utilization of gamma-amino butyrate {{PubMed\|24142252}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU06310&redirect=T BSU06310]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gabP.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11328]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** uptake of gamma-amino butyrate {{PubMed\|24142252}}
−	** minor transporter for proline (allows growth with proline in the absence of the major [[transporters]] [[PutP]] and [[OpuE]]) {{PubMed\|24142252}}
−
−	* '''Protein family:'''
−	** secondary amino acid transporter
−	** [[APC superfamily of transport proteins\|amino acid, polyamine, organocation (APC) superfamily of transporters]], [http://www.tcdb.org/search/result.php?tc=2.A.3 TC 2.A.3]
−	* '''Paralogous protein(s):''' [[AapA]], [[HutM]], [[RocC]], [[RocE]], [[YbgF]], [[YbxG]], [[YdgF]], [[YtnA]], [[YvbW]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−	** K(M) for gamma-amino butyrate: 77 +/- 17 µM {{PubMed\|24142252}}
−	** K(M) for proline: 700 +/- 330 µM {{PubMed\|24142252}}
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** cell membrane (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU06310&redirect=T BSU06310]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P46349 P46349]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06310]
−
−	* '''[http://www.tcdb.org/ T.C.] number:''' [http://www.tcdb.org/search/result.php?tc=2.A.3.1.5 2.A.3.1.5]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''gabP'' {{PubMed\|8951816}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gabP_685155_686564_-1 gabP] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|8951816}}
−
−	* '''Regulation:'''
−	** expressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8951816 PubMed]
−	** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8951816 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[TnrA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/8951816 PubMed]
−	** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/8951816 PubMed]
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 178 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** available in [[Erhard Bremer]]'s lab {{PubMed\|24142252}}
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>8951816, 9677314, 24142252 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:58, 17 April 2014
Line 132:		Line 132:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 178 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gabP.html]
@@ Line 102: / Line 103: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 15: / Line 15: @@
 |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=BSU06310 gabP]
 |-
-|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/ala_gly_ser.html Ala, Gly, Ser]'''
+|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=gabP gabP]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 9.45

@@ Line 79: / Line 79: @@
 * '''Protein family:'''
 ** secondary amino acid transporter
-** amino acid, polyamine, organocation (APC) family of transporters, [http://www.tcdb.org/search/result.php?tc=2.A.3 TC 2.A.3]
+** [[APC superfamily of transport proteins|amino acid, polyamine, organocation (APC) superfamily of transporters]], [http://www.tcdb.org/search/result.php?tc=2.A.3 TC 2.A.3]
 * '''Paralogous protein(s):''' [[AapA]], [[HutM]], [[RocC]], [[RocE]], [[YbgF]], [[YbxG]], [[YdgF]], [[YtnA]], [[YvbW]]

@@ Line 110: / Line 110: @@
 * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU06310]
-* '''T.C. number:''' [http://www.tcdb.org/search/result.php?tc=2.A.3.1.5 2.A.3.1.5]
+* '''[http://www.tcdb.org/ T.C.] number:''' [http://www.tcdb.org/search/result.php?tc=2.A.3.1.5 2.A.3.1.5]
 === Additional information===

@@ Line 77: / Line 77: @@
 ** minor transporter for proline (allows growth with proline in the absence of the major [[transporters]] [[PutP]] and [[OpuE]]) {{PubMed|24142252}}
-* '''Protein family:''' secondary amino acid transporter
+* '''Protein family:'''
 * '''Paralogous protein(s):''' [[AapA]], [[HutM]], [[RocC]], [[RocE]], [[YbgF]], [[YbxG]], [[YdgF]], [[YtnA]], [[YvbW]]

← Older revision		Revision as of 12:20, 28 November 2013
Line 133:		Line 133:

	* '''Mutant:'''		* '''Mutant:'''
		+	** available in [[Erhard Bremer]]'s lab {{PubMed\|24142252}}

	* '''Expression vector:'''		* '''Expression vector:'''