DarA - Revision history

Jstuelk: /* References */

2015-04-17T15:54:32Z

‎References

Jgundlach: /* Biological materials */

2015-04-01T12:24:32Z

‎Biological materials

Jstuelk: /* Database entries */

2015-01-16T09:08:34Z

‎Database entries

Jstuelk at 10:28, 30 November 2014

2014-11-30T10:28:05Z

Jstuelk: /* Database entries */

2014-11-26T10:26:19Z

‎Database entries

Jstuelk: /* Database entries */

2014-11-26T10:25:47Z

‎Database entries

Jstuelk: /* Expression and regulation */

2014-11-10T12:56:54Z

‎Expression and regulation

Jstuelk at 12:55, 10 November 2014

2014-11-10T12:55:48Z

Jstuelk: Jstuelk moved page YaaQ to DarA: Gundlach et al., JBC

2014-11-10T12:54:35Z

Jstuelk moved page YaaQ to DarA: Gundlach et al., JBC

Jstuelk: /* Biological materials */

2014-09-24T13:02:53Z

‎Biological materials

← Older revision		Revision as of 15:54, 17 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' c-di-AMP-binding PII-like protein<br/><br/>~~	+	{{#bank: DarA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''darA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yaaQ ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\|~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| c-di-AMP-binding PII-like protein~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| unknown~~
−	\|-
−	\|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=BSU00290 darA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 11 kDa, 6.088~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 327 bp, 109 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[tmk]]'', ''[[yaaR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00290 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yaaQ_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=yaaQ_39871_40200_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yaaQ_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00290]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[proteins of unknown function]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00290
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00290&redirect=T BSU00290]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10093]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−	** binds c-di-AMP {{PubMed\|25433025}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** forms homo-trimers {{PubMed\|25433025}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00290&redirect=T BSU00290]
−
−	* '''Structure:'''
−	** [http://www.pdb.org/pdb/explore/explore.do?structureId=4RLE 4RLE] (the ''B. subtilis'' protein in complex with c-di-AMP) {{PubMed\|25433025}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37538 P37538]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00290]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[darA]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaQ_39871_40200_1 darA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 1030 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 922 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 894 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−	** GP1712 (''[[darA]]''::''cat''), available in [[Jörg Stülke]]'s lab {{PubMed\|25433025}}
−	** GP1713 (''[[darA]]-[[yaaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−	** pGP2601: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab {{PubMed\|25433025}}
−	** pGP2624: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab
−	** pGP2603: expression of ''yaaQ''-Strep by [[pGP382]] in ''B. subtilis'' suitable for [[SPINE]], available in [[Jörg Stülke]]'s lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:''' available in [[Jörg Stülke]]'s lab
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed> 22383849 25433025 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 125: / Line 125: @@
 * '''Expression vector:'''
-**pGP2601: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab {{PubMed|25433025}}
+** pGP2601: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab {{PubMed|25433025}}
-**pGP2624: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab
+** pGP2624: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab
-**pGP2603: expression of ''yaaQ''-Strep by [[pGP382]] in ''B. subtilis'' suitable for [[SPINE]], available in [[Jörg Stülke]]'s lab
+** pGP2603: expression of ''yaaQ''-Strep by [[pGP382]] in ''B. subtilis'' suitable for [[SPINE]], available in [[Jörg Stülke]]'s lab
 * '''lacZ fusion:'''

@@ Line 93: / Line 93: @@
 * '''Structure:'''
 ** [http://www.pdb.org/pdb/explore/explore.do?structureId=4RLE 4RLE] (the ''B. subtilis'' protein in complex with c-di-AMP) {{PubMed|25433025}}
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P37538 P37538]

@@ Line 1: / Line 1: @@
-* '''Description:''' unknown <br/><br/>
+* '''Description:''' c-di-AMP-binding PII-like protein<br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' ||
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+|style="background:#ABCDEF;" align="center"| '''Product''' || c-di-AMP-binding PII-like protein
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || unknown
@@ Line 81: / Line 81: @@
 * '''Effectors of protein activity:'''
 * '''[[SubtInteract|Interactions]]:'''
-** forms homo-trimers (see [http://www.pdb.org/pdb/explore/explore.do?structureId=3m05 3M05])
+** forms homo-trimers {{PubMed|25433025}}
 * '''[[Localization]]:'''
@@ Line 91: / Line 92: @@
 * '''Structure:'''
-** [http://www.pdb.org/pdb/explore/explore.do?structureId=4RLE 4RLE] (the ''B. subtilis'' protein in complex with c-di-AMP)
+** [http://www.pdb.org/pdb/explore/explore.do?structureId=4RLE 4RLE] (the ''B. subtilis'' protein in complex with c-di-AMP) {{PubMed|25433025}}
 ** [http://www.pdb.org/pdb/explore/explore.do?structureId=3m05 3M05] (the apoprotein from ''Pediococcus pentosaceus'', 50% identity)
@@ Line 121: / Line 122: @@
 =Biological materials =
 * '''Mutant:'''
-** GP1712 (''[[darA]]''::''cat''), available in [[Jörg Stülke]]'s lab
+** GP1712 (''[[darA]]''::''cat''), available in [[Jörg Stülke]]'s lab {{PubMed|25433025}}
 ** GP1713 (''[[darA]]-[[yaaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''
-**pGP2601: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab
+**pGP2601: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]], available in [[Jörg Stülke]]'s lab {{PubMed|25433025}}
 **pGP2624: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab
 **pGP2603: expression of ''yaaQ''-Strep by [[pGP382]] in ''B. subtilis'' suitable for [[SPINE]], available in [[Jörg Stülke]]'s lab
@@ Line 142: / Line 143: @@
 =References=
-<pubmed> 22383849</pubmed>
+<pubmed> 22383849  25433025 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 92: / Line 92: @@
 * '''Structure:'''
 ** [http://www.pdb.org/pdb/explore/explore.do?structureId=4RLE 4RLE] (the ''B. subtilis'' protein in complex with c-di-AMP)
-** [http://www.pdb.org/pdb/explore/explore.do?structureId=3m05 3M05] (the protein from ''Pediococcus pentosaceus'', 50% identity)
+** [http://www.pdb.org/pdb/explore/explore.do?structureId=3m05 3M05] (the apoprotein from ''Pediococcus pentosaceus'', 50% identity)
 * '''UniProt:''' [http://www.uniprot.org/uniprot/P37538 P37538]

← Older revision		Revision as of 10:25, 26 November 2014
Line 91:		Line 91:

	* '''Structure:'''		* '''Structure:'''
		+	** [http://www.pdb.org/pdb/explore/explore.do?structureId=4RLE 4RLE] (the ''B. subtilis'' protein in complex with c-di-AMP)
	** [http://www.pdb.org/pdb/explore/explore.do?structureId=3m05 3M05] (the protein from ''Pediococcus pentosaceus'', 50% identity)		** [http://www.pdb.org/pdb/explore/explore.do?structureId=3m05 3M05] (the protein from ''Pediococcus pentosaceus'', 50% identity)

@@ Line 103: / Line 103: @@
 =Expression and regulation=
-* '''Operon:''' ''[[yaaQ]]-[[darA]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}
+* '''Operon:''' ''[[darA]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaQ_39871_40200_1 darA] {{PubMed|22383849}}

@@ Line 4: / Line 4: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''yaaQ''
+|''darA''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaQ ''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' ||
@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 |-
-|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=BSU00290 yaaQ]
+|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=BSU00290 darA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 6.088
@@ Line 103: / Line 103: @@
 =Expression and regulation=
-* '''Operon:''' ''[[yaaQ]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}
+* '''Operon:''' ''[[yaaQ]]-[[darA]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaQ_39871_40200_1 yaaQ] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaQ_39871_40200_1 darA] {{PubMed|22383849}}
 * '''[[Sigma factor]]:'''
@@ Line 120: / Line 120: @@
 =Biological materials =
 * '''Mutant:'''
-** GP1712 (''[[yaaQ]]''::''cat''), available in [[Jörg Stülke]]'s lab
+** GP1712 (''[[darA]]''::''cat''), available in [[Jörg Stülke]]'s lab
-** GP1713 (''[[yaaQ]]-[[yaaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
+** GP1713 (''[[darA]]-[[yaaR]]''::''cat''), available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''

← Older revision	Revision as of 12:54, 10 November 2014
(No difference)