OppA - Revision history

Jstuelk: /* References */

2015-07-30T08:26:02Z

‎References

Jstuelk: /* Biological materials */

2015-07-20T08:42:43Z

‎Biological materials

Jstuelk: /* Biological materials */

2015-07-20T08:42:24Z

‎Biological materials

Jstuelk at 13:26, 15 May 2015

2015-05-15T13:26:08Z

Jstuelk: /* References */

2015-03-20T14:35:35Z

‎References

134.76.70.252 at 09:55, 17 April 2014

2014-04-17T09:55:39Z

134.76.70.252 at 11:51, 8 April 2014

2014-04-08T11:51:12Z

134.76.38.147 at 13:24, 2 April 2014

2014-04-02T13:24:47Z

Jstuelk: /* References */

2013-12-28T10:32:09Z

‎References

134.76.70.252 at 16:00, 11 November 2013

2013-11-11T16:00:22Z

← Older revision		Revision as of 08:26, 30 July 2015
Line 1:		Line 1:
−	* '''Description:''' oligopeptide [[ABC transporter]] (binding protein) <br/><br/>	+	{{#bank: OppA}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:~~#~~ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''oppA''~~
−	\|-
−	~~\|style="background~~:~~#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''spo0KA ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| oligopeptide [[ABC transporter]] (binding protein)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| initiation of sporulation, competence development~~
−	\|-
−	\|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=BSU11430 oppA]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=OppA ~~OppA]~~
−	\|-
−	\|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=OppA OppA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 61 kDa, 5.722~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1635 bp, 545 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[trpS]]'', ''[[oppB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU11430 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU11430 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU11430 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:oppA_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=oppA_1219849_1221486_1 Expression at a glance]'''   {{PubMed\|22383849}~~}~~<br/>[[Image:oppA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU11430]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[ABC transporters]]}},~~
−	~~{{SubtiWiki category\|[[utilization of nitrogen sources other than amino acids]]}},~~
−	~~{{SubtiWiki category\|[[genetic competence]]}},~~
−	~~{{SubtiWiki category\|[[phosphorelay]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CodY regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[ScoC regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[TnrA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU11430
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU11430&redirect=T BSU11430]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/oppABCDF.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10771]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** required for the uptake of quorum sensing peptides such as [[PhrH]] {{PubMed\|21908671}}
−
−	* '''Protein family:''' bacterial solute-binding protein 5 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[DppE]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:''' phosphorylation on (Tyr-301 OR Tyr-303) AND Thr-470 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** ([[OppD]]-[[OppF]])-([[OppB]]-[[OppC]])-[[OppA]] {{PubMed\|10092453}}
−	** [[FloT]]-[[OppA]] {{PubMed\|23651456}}
−
−	* '''[[Localization]]:'''
−	** attached to the cell membrane (via [[OppB]]-[[OppC]]) {{PubMed\|10092453}}
−	** at the outer side of the cell: extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], lipid modification as retention signal [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU11430&redirect=T BSU11430]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P24141 P24141]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU11430]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[oppA]]-[[oppB]]-[[oppC]]-[[oppD]]-[[oppF]]'' {{PubMed\|1901616}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=oppA_1219849_1221486_1 oppA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−	** expressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
−	** repressed during exponential growth ([[ScoC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[TnrA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
−	** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]
−	** [[CodY]]: transcription repression, no derepression occurs, however, in a ''[[codY]]'' mutant, due to increased repression by [[ScoC]] {{PubMed\|25966844}}
−
−	* '''Additional information:'''
−	** A [[ncRNA]] is predicted between ''[[trpS]]'' and ''[[oppA]]'' {{PubMed\|20525796}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1937 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 20139 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** BP67 (spc) available in [[Fabian Commichau]]'s lab
−	** 1S118 ( ''oppA''::''spec''), {{PubMed\|11267663}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S118&Search=1S118 BGSC]
−	** GP2097 (D(''[[oppA]]-[[oppB]]-[[oppC]]-[[oppD]]-[[oppF]]'')::''aphA3''), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>1901616,10092453,12823818,11267663,9252573,10960106,,12823818,10383984,18957862 18763711 17218307, 7997159 20525796 23651456 21908671 25966844 1899858 23199363</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 140: / Line 140: @@
 ** BP67 (spc) available in [[Fabian Commichau]]'s lab
 ** 1S118 ( ''oppA''::''spec''), {{PubMed|11267663}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S118&Search=1S118 BGSC]
-** GP2097 (D(''[[oppA]]-[[oppB]]-[[oppC]]-[[oppD]]-[[oppE]]'')::''aphA3''), available in [[Jörg Stülke]]'s lab
+** GP2097 (D(''[[oppA]]-[[oppB]]-[[oppC]]-[[oppD]]-[[oppF]]'')::''aphA3''), available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''

@@ Line 140: / Line 140: @@
 ** BP67 (spc) available in [[Fabian Commichau]]'s lab
 ** 1S118 ( ''oppA''::''spec''), {{PubMed|11267663}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S118&Search=1S118 BGSC]
 * '''Expression vector:'''

@@ Line 48: / Line 48: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[ScoC regulon]]}},
 {{SubtiWiki regulon|[[TnrA regulon]]}}
@@ Line 127: / Line 128: @@
 ** [[TnrA]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
 ** [[ScoC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/10383984 PubMed]
 * '''Additional information:'''
@@ Line 135: / Line 137: @@
 =Biological materials =
-* '''Mutant:''' BP67 (spc) available in [[Fabian Commichau]]'s lab
+* '''Mutant:'''
 ** 1S118 ( ''oppA''::''spec''), {{PubMed|11267663}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1S118&Search=1S118 BGSC]
@@ Line 153: / Line 156: @@
 =References=
-<pubmed>1901616,10092453,12823818,11267663,9252573,10960106,,12823818,10383984,18957862 18763711 17218307, 7997159 20525796 23651456 21908671 1899858 23199363</pubmed>
+<pubmed>1901616,10092453,12823818,11267663,9252573,10960106,,12823818,10383984,18957862 18763711 17218307, 7997159 20525796 23651456 21908671 25966844 1899858 23199363</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 153: / Line 153: @@
 =References=
-<pubmed>1901616,10092453,12823818,11267663,9252573,10960106,,12823818,10383984,18957862 18763711 17218307, 7997159 20525796 23651456 21908671 23199363</pubmed>
+<pubmed>1901616,10092453,12823818,11267663,9252573,10960106,,12823818,10383984,18957862 18763711 17218307, 7997159 20525796 23651456 21908671 1899858 23199363</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 16: / Line 16: @@
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=OppA OppA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.722

@@ Line 58: / Line 58: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/oppABCDF.html]
@@ Line 97: / Line 98: @@
 === 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=BSU11430 oppA]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/OppA OppA]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=OppA OppA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.722