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

N Ogasawara, S Moriya, H Yoshikawa
Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.
Nucleic Acids Res: 1985, 13(7);2267-79
[PubMed:2987848] [WorldCat.org] [DOI] (P p)

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