YabA - Revision history

Jstuelk at 12:58, 10 November 2014

2014-11-10T12:58:33Z

134.76.70.252 at 10:10, 17 April 2014

2014-04-17T10:10:43Z

134.76.38.147 at 12:45, 2 April 2014

2014-04-02T12:45:51Z

Jstuelk at 11:25, 27 November 2013

2013-11-27T11:25:35Z

134.76.70.252 at 14:56, 11 November 2013

2013-11-11T14:56:53Z

Jstuelk at 16:46, 8 August 2013

2013-08-08T16:46:31Z

Jstuelk: /* Original publications */

2013-08-08T16:15:49Z

‎Original publications

134.76.70.252 at 12:17, 16 May 2013

2013-05-16T12:17:52Z

134.76.70.252 at 09:08, 14 May 2013

2013-05-14T09:08:22Z

134.76.70.252 at 11:54, 13 May 2013

2013-05-13T11:54:28Z

← Older revision		Revision as of 12:58, 10 November 2014
Line 1:		Line 1:
−	* '''Description:~~''' inhibitor of [[DnaA]] oligomerization, tethers [[DnaA]] to the polymerase-clamp protein [[DnaN]] <br/><br/>~~	+	{{#bank: YabA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yabA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| negative regulator of replication initiation~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| positioning of [[DnaA]]~~
−	\|-
−	\|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=BSU00330 yabA]
−	\|-
−	\|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=YabA YabA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 13 kDa, 6.065~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 357 bp, 119 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yaaT]]'', ''[[yabB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00330 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yabA_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=yabA_42499_42858_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yabA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00330]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[DNA replication]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00330
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~strongly reduced growth rate in minimal medium [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00330&redirect=T BSU00330]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10097]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** negative control of replication initiation {{PubMed\|12060778}}
−	** associates with the ''oriC'' region in a [[DnaA]]-dependent manner, this limits the amount of [[DnaA]] that can bind the ''oriC'' region {{PubMed\|21895792}}
−	** YabA inhibits co-operative DNA binding by [[DnaA]] {{PubMed\|21895792}}
−	** inhibits oligomerization and helix formation of [[DnaA]] {{PubMed\|23909787}}
−
−	* '''Protein family:''' yabA family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:''' leucine zipper
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):''' Zn cluster
−
−	* '''Effectors of protein activity:'''
−	** [[DnaN]] overexpression or release from the replisome decreases association of [[YabA]] with ''oriC'', increases association of [[DnaA]] with ''oriC'' {{PubMed\|21895792}}
−
−	* '''[[SubtInteract\|Interactions]]:''' [[DnaA]]-[[YabA]]-[[DnaN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed]
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00330&redirect=T BSU00330]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37542 P37542]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00330]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[yaaQ]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yabA_42499_42858_1 yabA] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 199 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−	~~[[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 Homepage]<br>~~
−	~~[[Alan Grossman]], Cambridge, MA, USA [http://web.mit.edu/biology/www/facultyareas/facresearch/grossman.html Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 20157337 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed> 19578359, 21895792,12060778 16461910, 19737352 19081080 23909787 22383849</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 10:10, 17 April 2014
Line 122:		Line 122:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 199 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 96: / Line 97: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 109: / Line 109: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''' ''[[yaaQ]]-[[yaaR]]-[[holB]]-[[yaaT]]-[[yabA]]-[[yabB]]-[[yazA]]-[[yabC]]'' {{PubMed|22383849}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yabA_42499_42858_1 yabA] {{PubMed|22383849}}
@@ Line 145: / Line 145: @@
 <pubmed> 20157337 </pubmed>
 ==Original publications==
-<pubmed> 19578359, 21895792,12060778 16461910, 19737352 19081080 23909787 </pubmed>
+<pubmed> 19578359, 21895792,12060778 16461910, 19737352 19081080 23909787 22383849</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=BSU00330 yabA]
 |-
-|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/YabA YabA]
+|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=YabA YabA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 6.065

@@ Line 1: / Line 1: @@
-* '''Description:''' tethers [[DnaA]] to the polymerase-clamp protein [[DnaN]] <br/><br/>
+* '''Description:''' inhibitor of [[DnaA]] oligomerization, tethers [[DnaA]] to the polymerase-clamp protein [[DnaN]] <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 76: / Line 72: @@
 ** associates with the ''oriC'' region in a [[DnaA]]-dependent manner, this limits the amount of [[DnaA]] that can bind the ''oriC'' region  {{PubMed|21895792}}
 ** YabA inhibits co-operative DNA binding by [[DnaA]] {{PubMed|21895792}}
 * '''Protein family:''' yabA family (according to Swiss-Prot)

@@ 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=yabA_42499_42858_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yabA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yabA_42499_42858_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yabA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00330]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaT]]'', ''[[yabB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00330 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00330 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yabA_context.gif]]