HolB - Revision history

Jgundlach: /* Biological materials */

2015-04-01T11:30:28Z

‎Biological materials

Jgundlach: /* Biological materials */

2015-04-01T11:24:06Z

‎Biological materials

Jstuelk at 12:58, 10 November 2014

2014-11-10T12:58:04Z

134.76.38.147 at 12:45, 2 April 2014

2014-04-02T12:45:46Z

Jstuelk at 11:25, 27 November 2013

2013-11-27T11:25:48Z

134.76.70.252 at 14:56, 11 November 2013

2013-11-11T14:56:47Z

134.76.70.252 at 12:17, 16 May 2013

2013-05-16T12:17:45Z

134.76.70.252 at 09:08, 14 May 2013

2013-05-14T09:08:14Z

134.76.70.252 at 11:54, 13 May 2013

2013-05-13T11:54:06Z

Jstuelk at 18:21, 27 March 2013

2013-03-27T18:21:20Z

← Older revision		Revision as of 11:30, 1 April 2015
Line 1:		Line 1:
−	* '''Description:~~''' DNA polymerase III (delta' subunit), part of the clamp-loader complex and the [[replisome]] <br/><br/>~~	+	{{#bank: HolB}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''holB''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''yaaS ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| DNA polymerase III (delta' subunit)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[DNA replication]]~~
−	\|-
−	\|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=BSU00310 holB]
−	\|-
−	\|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=HolB HolB]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 37 kDa, 6.334~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 987 bp, 329 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yaaR]]'', ''[[yaaT]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00310 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00310 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00310 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:holB_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=holB_40665_41654_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:holB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00310]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[DNA replication]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU00310
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00310&redirect=T BSU00310]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10095]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
−	** required for bacteriophage SPP1 replication {{PubMed\|23268446}}
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[DnaX]](3)-[[HolA]]-[[HolB]], the clamp-loader complex {{PubMed\|23525462}}
−	** part of the [[replisome]]: [[PolC]]-[[HolA]]-[[HolB]]-[[DnaX]]-[[DnaN]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[SsbA]]-[[DnaE]]-[[PriA]]-[[DnaB]] {{PubMed\|20122408}}
−
−	* '''[[Localization]]:'''
−	** forms foci {{PubMed\|21958350}}
−	** cytoplasm (homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00310&redirect=T BSU00310]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P37540 P37540]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00310]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.7 2.7.7.7]
−
−	~~=== 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=holB_40665_41654_1 holB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>23268446,21958350 16479537 20122408 23525462 22383849</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 134: / Line 134: @@
 * '''GFP fusion:'''
-* '''two-hybrid system:'''
+* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
 * '''Antibody:'''

@@ Line 64: / Line 64: @@
 === Additional information===
 =The protein=
@@ Line 115: / Line 112: @@
 =Expression and regulation=
-* '''Operon:''' ''[[yaaQ]]-[[yaaR]]-[[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=holB_40665_41654_1 holB] {{PubMed|22383849}}

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 100: / Line 101: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 113: / Line 113: @@
 =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=holB_40665_41654_1 holB] {{PubMed|22383849}}
@@ Line 144: / Line 144: @@
 =References=
-<pubmed>23268446,21958350 16479537 20122408 23525462</pubmed>
+<pubmed>23268446,21958350 16479537 20122408 23525462 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=BSU00310 holB]
 |-
-|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/HolB HolB]
+|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=HolB HolB]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 6.334

@@ 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=holB_40665_41654_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:holB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=holB_40665_41654_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:holB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00310]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaR]]'', ''[[yaaT]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00310 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00310 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00310 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00310 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00310 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00310 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:holB_context.gif]]

@@ Line 1: / Line 1: @@
-* '''Description:''' DNA polymerase III (delta subunit), part of the [[replisome]] <br/><br/>
+* '''Description:''' DNA polymerase III (delta' subunit), part of the clamp-loader complex and the [[replisome]] <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase III (delta subunit)
+|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase III (delta' subunit)
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]