SpoIIAA - Revision history

Jstuelk: /* Expression and regulation */

2015-04-06T14:39:16Z

‎Expression and regulation

134.76.70.252 at 14:14, 17 April 2014

2014-04-17T14:14:51Z

134.76.38.147 at 14:07, 2 April 2014

2014-04-02T14:07:50Z

134.76.70.252 at 11:08, 7 January 2014

2014-01-07T11:08:26Z

134.76.70.252 at 08:46, 12 November 2013

2013-11-12T08:46:39Z

Jstuelk: /* References */

2013-09-27T08:06:48Z

‎References

Jstuelk at 20:32, 18 June 2013

2013-06-18T20:32:44Z

134.76.70.252 at 13:49, 16 May 2013

2013-05-16T13:49:42Z

134.76.70.252 at 10:38, 14 May 2013

2013-05-14T10:38:13Z

134.76.70.252 at 13:12, 13 May 2013

2013-05-13T13:12:45Z

← Older revision		Revision as of 14:39, 6 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' anti-anti-[[SigF]] <br/><br/>~~	+	{{#bank: SpoIIAA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''spoIIAA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| anti-anti-[[SigF]]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of [[SigF]] activity~~
−	\|-
−	\|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=BSU23470 spoIIAA]
−	\|-
−	\|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=SpoIIAA SpoIIAA]
−	\|-
−	\|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=spoIIAA spoIIAA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 12 kDa, 5.855~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 351 bp, 117 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[spoIIAB]]'', ''[[dacF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23470 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:spoIIAA_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=spoIIAA_2444645_2444998_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:spoIIAA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23470]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[sigma factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[sporulation proteins]]}},~~
−	~~{{SubtiWiki category\|[[phosphoproteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigF regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigG regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SigH regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[SinR regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU23470
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23470&redirect=T BSU23470]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacF-spoIIAAB-sigF.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10296]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' anti-sigma-factor antagonist family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:''' phosphorylation on (Ser-58 OR Ser-59) by [[SpoIIAB]][http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[SpoIIAB]]-[[SpoIIAA]] {{PubMed\|15201047}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU23470&redirect=T BSU23470]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1TIL 1TIL] (complex with SpoIIAB, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=1AUZ 1AUZ] (NMR)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P10727 P10727]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23470]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−	** ''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
−	** ''[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spoIIAA_2444645_2444998_-1 spoIIAA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−	** ''[[dacF]]'': [[SigF]], [[SigG]]
−	** ''[[spoIIAA]]'': [[SigH]]
−
−	* '''Regulation:''' repressed by glucose (5.2-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], ''[[dacF]]'': expressed during sporulation, ''[[spoIIAA]]'': expressed early during sporulation
−	** expressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1556084,15687200 PubMed]
−
−	* '''Regulatory mechanism:''' ''[[spoIIAA]]'': activated by [[Spo0A]] and repressed by [[SinR]]
−	** [[Spo0A]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/1556084,15687200 PubMed]
−	** [[AbrB]]: transcription repression {{PubMed\|20817675}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 388 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 237 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3471 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	* [[Tony Wilkinson]], York University, U.K. [http://www.york.ac.uk/depts/chem/staff/ajw.html homepage]
−	* [[Charles Moran]], Emory University, NC, USA [http://www.microbiology.emory.edu/moran_c.html homepage]
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Modeling of [[SigF]] activation==~~
−	~~<pubmed> 24067622 22312331 20298743</pubmed>~~
−	~~==Original Publications==~~
−	<pubmed>1391042,8358793,8955289,15023063,15351644,9077448,10323866,8820658,8622920,16824103,7570023,10476035,8932322,8764398,8764397,12676949,9826498,9826499,14744853,9642177,11684022,8846916,11298272,1948031,3114419,11846550,15201047,2123551,8168129,,1556084,15687200,12850135 16493705 17218307, 10049355 20817675,</pubmed>
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 134: / Line 134: @@
 * '''Additional information:'''
 =Biological materials =
 * '''Mutant:'''

@@ Line 63: / Line 63: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacF-spoIIAAB-sigF.html]
@@ Line 101: / Line 102: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1TIL 1TIL] (complex with SpoIIAB, Geobacillus stearothermophilus),  [http://www.rcsb.org/pdb/explore.do?structureId=1AUZ 1AUZ] (NMR)

@@ Line 18: / Line 18: @@
 |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=SpoIIAA SpoIIAA]
 |-
-|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/stress_response.html Stress]'''
+|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=spoIIAA spoIIAA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 5.855

@@ 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=BSU23470 spoIIAA]
 |-
-|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/SpoIIAA SpoIIAA]
+|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=SpoIIAA SpoIIAA]
 |-
 |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/stress_response.html Stress]'''

@@ Line 155: / Line 155: @@
 =References=
-<pubmed>1391042,8358793,8955289,15023063,15351644,9077448,10323866,8820658,8622920,16824103,7570023,10476035,8932322,8764398,8764397,12676949,9826498,9826499,14744853,9642177,11684022,8846916,11298272,1948031,3114419,11846550,15201047,2123551,8168129,,1556084,15687200,12850135 16493705 17218307, 20298743 10049355 20817675,22312331</pubmed>
+==Modeling of [[SigF]] activation==
 [[Category:Protein-coding genes]]

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 124: / Line 120: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spoIIAA_2444645_2444998_-1 spoIIAA] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 ** ''[[dacF]]'': [[SigF]], [[SigG]]
 ** ''[[spoIIAA]]'': [[SigH]]
@@ Line 159: / Line 155: @@
 =References=
-'''Additional publications:''' {{PubMed|20817675,22312331}}
+<pubmed>1391042,8358793,8955289,15023063,15351644,9077448,10323866,8820658,8622920,16824103,7570023,10476035,8932322,8764398,8764397,12676949,9826498,9826499,14744853,9642177,11684022,8846916,11298272,1948031,3114419,11846550,15201047,2123551,8168129,,1556084,15687200,12850135 16493705 17218307, 20298743 10049355 20817675,22312331</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 31: / Line 31: @@
   <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=spoIIAA_2444645_2444998_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:spoIIAA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=spoIIAA_2444645_2444998_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:spoIIAA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU23470]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoIIAB]]'', ''[[dacF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23470 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU23470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU23470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU23470 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:spoIIAA_context.gif]]