YydF - Revision history

134.76.38.147 at 15:15, 2 April 2014

2014-04-02T15:15:42Z

Jstuelk: /* Original publications */

2013-12-28T10:32:29Z

‎Original publications

134.76.70.252 at 09:46, 12 November 2013

2013-11-12T09:46:53Z

Jstuelk: /* Original publications */

2013-07-13T16:26:50Z

‎Original publications

134.76.70.252 at 15:01, 16 May 2013

2013-05-16T15:01:07Z

134.76.70.252 at 11:43, 14 May 2013

2013-05-14T11:43:46Z

134.76.70.252 at 14:18, 13 May 2013

2013-05-13T14:18:38Z

Jstuelk: /* Extended information on the protein */

2012-10-31T13:45:23Z

‎Extended information on the protein

Jstuelk at 13:39, 31 October 2012

2012-10-31T13:39:32Z

Jstuelk at 13:36, 31 October 2012

2012-10-31T13:36:59Z

← Older revision		Revision as of 15:15, 2 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' secreted peptide, controls [[LiaR]]-[[LiaS]] activity <br/><br/>~~	+	{{#bank: YydF}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yydF''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| secreted peptide~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| control of [[LiaR]]-[[LiaS]] 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=BSU40180 yydF]
−	\|-
−	\|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=YydF YydF]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 5 kDa, 9.567~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 147 bp, 49 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yydG]]'', ''[[fbp]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40180 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40180 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40180 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yydF_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=yydF_4127498_4127647_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yydF_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40180]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU40180
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yydFGHIJ.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11479]
−
−	~~=== 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:'''
−	** modified by [[YydG]] {{PubMed\|23106164}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[YydF]]-[[YydG]] {{PubMed\|23106164}}
−	** [[YydF]]-[[YydH]] {{PubMed\|23106164}}
−
−	* '''[[Localization]]:'''
−	** extracellular (processing requires [[YydH]], transport by [[YydI]]-[[YydJ]]) {{PubMed\|23106164}}
−
−	~~=== Database entries ===~~
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/Q45596 Q45596]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40180]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[yydF]]-[[yydG]]-[[yydH]]-[[yydI]]-[[yydJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yydF_4127498_4127647_-1 yydF] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
−
−	* '''Regulation:'''
−	** activated after transition to stationary phase([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
−
−	* '''Additional information:'''
−	** the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
−	** the ''yydF'' portion of the mRNA belongs to the most stable mRNAs in ''B. subtilis'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17921301 PubMed]
−	** the amount of the mRNA is substantially decreased upon depletion of [[Rny\|RNase Y]] {{PubMed\|21815947}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 23106164</pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>12884008,,17921301,17921301,21815947 23199363</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 147: / Line 147: @@
 <pubmed> 23106164</pubmed>
 ==Original publications==
-<pubmed>12884008,,17921301,17921301,21815947</pubmed>
+<pubmed>12884008,,17921301,17921301,21815947 23199363</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=BSU40180 yydF]
 |-
-|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/YydF YydF]
+|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=YydF YydF]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 9.567

@@ Line 147: / Line 147: @@
 <pubmed> 23106164</pubmed>
 ==Original publications==
- <big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J''  </big>
+<pubmed>12884008,,17921301,17921301,21815947</pubmed>
 [[Category:Protein-coding genes]]

@@ 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=yydF_4127498_4127647_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yydF_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yydF_4127498_4127647_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yydF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU40180]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yydG]]'', ''[[fbp]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40180 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40180 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40180 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU40180 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU40180 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU40180 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yydF_context.gif]]

@@ Line 92: / Line 92: @@
 * '''[[Localization]]:'''
-** extracellular (processing requires [[YydH]]) {{PubMed|23106164}}
+** extracellular (processing requires [[YydH]], transport by [[YydI]]-[[YydJ]]) {{PubMed|23106164}}
 === Database entries ===

@@ Line 15: / Line 15: @@
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40180 yydF]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 9.567