Difference between revisions of "Sandbox"

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* '''Description:''' DNA polymerase  III (gamma and tau subunits) part of the clamp-loader complex and the [[replisome]] <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'''
−
|''dnaX''
+
|''yaaK''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dna-8132 ''
+
|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''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase  III (gamma and tau subunits)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
+
|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=BSU00190 dnaX]
+
|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=BSU00200 yaaK]
 
|-
 
|-
−
|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=DnaX DnaX]
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 4.536 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.488 
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 321 bp, 107 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1689 bp, 563 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaX]]'', ''[[recR]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[scr]]'', ''[[yaaK]]''
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00200 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00200 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00200 DNA_with_flanks]
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00190 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00190 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00190 DNA_with_flanks]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaK_context.gif]]
−
|-
 
−
|-
 
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaX_context.gif]]
 
 
  <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=dnaX_26814_28505_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:dnaX_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00190]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaK_28529_28852_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaK_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00200]]
 
|-
 
|-
 
|}
 
|}
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<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
 +
 
<br/><br/>
 
<br/><br/>
  
 
= [[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]] =
Line 52: Line 51:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00190
+
* '''Locus tag:''' BSU00200
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 62: Line 59:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10083]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10084]
  
 
=== Additional information===
 
=== Additional information===
−
 
+
* The ''E.coli'' homolog: [http://ecoliwiki.net/colipedia/index.php/ybaB ''ybaB'']
−
 
 
−
 
 
  
 
=The protein=
 
=The protein=
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''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:'''
+
* '''Protein family:''' UPF0133 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
* '''The corresponding gene in ''E. coli'':''' [http://ecoliwiki.net/colipedia/index.php/ybaB EcoliWiki] {{PubMed|19594923}}
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
−
** [[DnaX]]-[[DnaB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 PubMed]
 
−
** [[DnaX]]-[[DnaC]] {{PubMed|23525462}}
 
−
** [[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]]:'''
 
* '''[[Localization]]:'''
−
** forms foci {{PubMed|21958350}}
 
−
** Nucleoid (Mid-cell) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 107: Line 96:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P09122 P09122]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P24281 P24281]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00190]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00200]
  
−
* '''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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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaX_26814_28505_1 dnaX] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaK_28529_28852_1 yaaK] {{PubMed|22383849}}
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 127: Line 116:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
  
 
=Biological materials =
 
=Biological materials =
Line 148: Line 137:
  
 
=References=
 
=References=
−
<pubmed> 16479537, 19415803, 14757052, 12974630 1703271, 12466528 20122408 23525462 23268446,21958350</pubmed>
+
 
 +
<pubmed>12884008,19594923, </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:54, 11 November 2013

  • Description: unknown

Gene name yaaK
Synonyms
Essential no
Product unknown
Function unknown
Gene expression levels in SubtiExpress: yaaK
MW, pI 11 kDa, 4.536
Gene length, protein length 321 bp, 107 aa
Immediate neighbours dnaX, recR
Sequences Protein DNA DNA_with_flanks
Genetic context
YaaK context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YaaK 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: BSU00200

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

  • The E.coli homolog: ybaB

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: UPF0133 family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information: the mRNA is very stable (half-life > 15 min) PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Anne E Cooley, Sean P Riley, Keith Kral, M Clarke Miller, Edward DeMoll, Michael G Fried, Brian Stevenson
DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family.
BMC Microbiol: 2009, 9;137
[PubMed:19594923] [WorldCat.org] [DOI] (I e)

G Hambraeus, C von Wachenfeldt, L Hederstedt
Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs.
Mol Genet Genomics: 2003, 269(5);706-14
[PubMed:12884008] [WorldCat.org] [DOI] (P p)

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