RpsF - Revision history

134.76.70.252 at 14:14, 17 April 2014

2014-04-17T14:14:09Z

134.76.70.252 at 09:28, 17 April 2014

2014-04-17T09:28:05Z

134.76.38.147 at 15:18, 2 April 2014

2014-04-02T15:18:32Z

Jstuelk at 14:44, 5 March 2014

2014-03-05T14:44:03Z

Jstuelk at 18:29, 13 December 2013

2013-12-13T18:29:56Z

134.76.70.252 at 09:49, 12 November 2013

2013-11-12T09:49:20Z

Jstuelk at 10:45, 19 June 2013

2013-06-19T10:45:47Z

134.76.70.252 at 15:03, 16 May 2013

2013-05-16T15:03:23Z

134.76.70.252 at 11:46, 14 May 2013

2013-05-14T11:46:10Z

134.76.70.252 at 14:20, 13 May 2013

2013-05-13T14:20:59Z

← Older revision		Revision as of 14:14, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' [[ribosomal protein]] <br/><br/>~~	+	{{#bank: RpsF}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''rpsF''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no {{PubMed\|23002217}}~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[ribosomal protein]] S6 (BS9)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[translation]]~~
−	\|-
−	\|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=BSU40910 rpsF]
−	\|-
−	\|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=RpsF RpsF]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 10 kDa, 4.993~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 285 bp, 95 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ssbA]]'', ''[[yyaF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40910 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:rpsF_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=rpsF_4199445_4199732_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:rpsF_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40910]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[translation]]}},~~
−	~~[[most abundant proteins]]~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[ComK regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[stringent response]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU40910
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40910&redirect=T BSU40910]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yyaF-rpsF-ssb-rpsR.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10049]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' [[ribosomal protein]] S6P family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[RpsF]]-[[RpsR]], the heterodimer binds the structure in the ''[[rpsF]]'' mRNA 5' UTR {{PubMed\|24310371}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU40910&redirect=T BSU40910]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3R3T 3R3T] (from ''Bacillus anthracis'', 71% identity, 97% similarity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P21468 P21468]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40910]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:'''
−	** ''[[yyaF]]-[[rpsF]]-[[ssbA]]-[[rpsR]]'' {{PubMed\|14762004}}
−	** ''[[rpsF]]-[[ssbA]]-[[rpsR]]'' {{PubMed\|24310371,22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rpsF_4199445_4199732_-1 rpsF] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−	** ''[[rpsF]]'': [[SigA]] {{PubMed\|24310371}}
−
−	* '''Regulation:'''
−	** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed\|11948165}}
−	** [[ComK]]: transcription activation {{PubMed\|11948146}}
−
−	* '''Additional information:'''
−	** the mRNA contains a structured motif in the 5' UTR upstream of the ''[[rpsF]]'' ORF that is bound by [[RpsF]]-[[RpsR]] heterodimers and may be implicated in autogenous regulation {{PubMed\|24310371}}
−	** belongs to the 100 [[most abundant proteins]] {{PubMed\|15378759}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 3469 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 4039 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>19653700 14762004 11948165 11948146 23002217 22383849 24310371 15378759</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 121: / Line 121: @@
 ** the mRNA contains a structured motif in the 5' UTR upstream of the ''[[rpsF]]'' ORF that is bound by [[RpsF]]-[[RpsR]] heterodimers and may be implicated in autogenous regulation {{PubMed|24310371}}
 ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
 =Biological materials =

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yyaF-rpsF-ssb-rpsR.html]
@@ Line 91: / Line 92: @@
 === Database entries ===
 * '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3R3T 3R3T] (from ''Bacillus anthracis'', 71% identity, 97% similarity)

@@ Line 40: / Line 40: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[translation]]}}
+{{SubtiWiki category|[[translation]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 61: / Line 62: @@
 === Additional information===
 =The protein=
@@ Line 120: / Line 118: @@
 * '''Additional information:'''
 ** the mRNA contains a structured motif in the 5' UTR upstream of the ''[[rpsF]]'' ORF that is bound by [[RpsF]]-[[RpsR]] heterodimers and may be implicated in autogenous regulation {{PubMed|24310371}}
 =Biological materials =
@@ Line 140: / Line 139: @@
 =References=
-<pubmed>19653700 14762004 11948165 11948146 23002217 22383849 24310371 </pubmed>
+<pubmed>19653700 14762004 11948165 11948146 23002217 22383849 24310371 15378759</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 79: / Line 79: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''
 * '''[[SubtInteract|Interactions]]:'''
 * '''[[Localization]]:'''
@@ Line 104: / Line 105: @@
 =Expression and regulation=
-* '''Operon:''' ''[[yyaF]]-[[rpsF]]-[[ssbA]]-[[rpsR]]'' {{PubMed|14762004}}
+* '''Operon:'''
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rpsF_4199445_4199732_-1 rpsF] {{PubMed|22383849}}
 * '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 115: / Line 119: @@
 * '''Additional information:'''
 =Biological materials =
@@ Line 135: / Line 140: @@
 =References=
-<pubmed>19653700 14762004 11948165 11948146 23002217</pubmed>
+<pubmed>19653700 14762004 11948165 11948146 23002217 22383849 24310371 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=BSU40910 rpsF]
 |-
-|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/RpsF RpsF]
+|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=RpsF RpsF]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 4.993

@@ Line 29: / Line 29: @@
   <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=rpsF_4199445_4199732_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rpsF_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rpsF_4199445_4199732_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rpsF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40910]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ssbA]]'', ''[[yyaF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40910 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40910 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:rpsF_context.gif]]