Difference between revisions of "Sandbox"

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−
* '''Description:''' DNA polymerase  III (beta subunit), beta clamp, part of the [[replisome]], also involved in DNA mismatch repair, inhibitor of [[DnaA]] oligomerization <br/><br/>
+
* '''Description:''' unknown <br/><br/>
 +
 
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''dnaN''
+
|''yaaA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaG, dnaK ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase  III <br/>(beta subunit), beta clamp
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]], DNA repair
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|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=BSU00020 DnaN]
+
|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=BSU00030 YaaA]
 
|-
 
|-
−
|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=DnaN DnaN]
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 4.332 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.718 
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 213 bp, 71 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1134 bp, 378 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaN]]'', ''[[recF]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaA]]'', ''[[yaaA]]''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00030 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00030 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00030 DNA_with_flanks]
−
|-
 
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00020 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00020 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00020 DNA_with_flanks]
 
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <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=dnaN_1939_3075_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:DnaN_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00020]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaA_3206_3421_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:YaaA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00030]]
 
|-
 
|-
 
|}
 
|}
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= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[DNA replication]]}},
+
{{SubtiWiki category|[[proteins of unknown function]]}}
−
{{SubtiWiki category|[[essential genes]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[Spo0A regulon]]}}
+
 
  
 
=The gene=
 
=The gene=
Line 49: Line 47:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00020
+
* '''Locus tag:''' BSU00030
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaA-recF-yaaB-gyrB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10066]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10067]
  
 
=== Additional information===
 
=== Additional information===
 +
 +
 +
  
 
=The protein=
 
=The protein=
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
−
** [[DnaN]] overexpression or release from the [[replisome]] decreases association of [[YabA]] with ''oriC'', increases association of [[DnaA]] with ''oriC'' {{PubMed|21895792}}
 
−
** Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)
 
−
** recruits [[MutS]] to the site of [[DNA replication]] ([[replisome]]) {{PubMed|23228104}}
 
−
** required for bacteriophage SPP1 replication {{PubMed|23268446}}
 
−
** inhibits oligomerization and helix formation of [[DnaA]] {{PubMed|23909787}}
 
  
 
* '''Protein family:'''
 
* '''Protein family:'''
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* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
−
** [[DnaA]]-[[YabA]]-[[DnaN]] {{PubMed|12060778}}
 
−
** part of the [[replisome]]: [[PolC]]-[[HolA]]-[[HolB]]-[[DnaX]]-[[DnaN]]-[[DnaG]]-[[DnaC]]-[[DnaI]]-[[DnaD]]-[[SsbA]]-[[DnaE]]-[[PriA]]-[[DnaB]] {{PubMed|20122408}}
 
−
** [[PolY1]]-[[DnaN]], [[PolY2]]-[[DnaN]] (required for untargeted mutagenesis) {{PubMed|15469515}}
 
−
** [[PolY1]]-[[PolA]]-[[DnaN]] {{PubMed|16045613}}
 
−
** [[MutL]] (C-terminal domain)-[[DnaN]] {{PubMed|21050827}}
 
−
** [[MutS]]-[[DnaN]] {{PubMed|20453097}}
 
−
** [[DnaE]]-[[DnaN]]  {{PubMed|21958350}}
 
−
** [[DnaN]] forms dimers {{PubMed|16045613}}
 
  
−
* '''[[Localization]]:'''  
+
* '''[[Localization]]:'''
−
** nucleoid (mid-cell spot) [http://www.ncbi.nlm.nih.gov/sites/entrez/9822387 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
−
** forms large assemblies on DNA, called "clamp zones" {{PubMed|21419346}}
 
−
** forms foci {{PubMed|21958350}}
 
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05649 P05649]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05650 P05650]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00020]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00030]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.7 2.7.7.7]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[dnaA]]-[[dnaN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:''' ''[[yaaA]]-[[recF]]-[[yaaB]]-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaN_1939_3075_1 dnaN] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaA_3206_3421_1 yaaA] {{PubMed|22383849}}
  
−
* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2987848}}
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Regulation:''' negatively controlled by [[DnaA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed] and [[Spo0A]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
+
* '''Regulation:'''  
−
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:''' [http://www.ncbi.nlm.nih.gov/sites/entrez/16942601 PubMed]  [http://www.ncbi.nlm.nih.gov/sites/entrez/9822387 PubMed]
+
* '''GFP fusion:'''
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
[[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
==Reviews==
+
 
−
<pubmed> 20157337 22933559 </pubmed>
+
<pubmed>2987848, </pubmed>
−
== Original publications ==
+
 
−
<pubmed>16942601 9822387 14651647,2987848 2168872 14651647 12060778 16461910, 16479537 19737352 19081080 11395445 20122408 20451384 15469515 16045613 21895792 20453097 23228104 23268446,21050827,21419346,21958350 23909787 </pubmed>
 
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:40, 11 November 2013

  • Description: unknown

Gene name yaaA
Synonyms
Essential
Product unknown
Function unknown
Gene expression levels in SubtiExpress: YaaA
MW, pI 7 kDa, 4.332
Gene length, protein length 213 bp, 71 aa
Immediate neighbours dnaN, recF
Sequences Protein DNA DNA_with_flanks
Genetic context
DnaA dnaN yaaA recF yaaB gyrB context.png
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YaaA expression.png















Categories containing this gene/protein

proteins of unknown function

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag: BSU00030

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

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:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

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