Difference between revisions of "Sandbox"

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−
* '''Description:''' general stress protein, survival of ethanol  stress, [[SafA]]-dependent protein of the inner spore coat, spore cortex lytic protein <br/><br/>
+
* '''Description:''' general stress protein, similar to isochorismatase <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'''
−
|''yaaH''
+
|''yaaI''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' sleL''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || N-acetylglucosaminidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of ethanol stress, protection of the spore
+
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of ethanol stress
 
|-
 
|-
−
|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=BSU00160 yaaH]
+
|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=BSU00170 yaaI]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.618  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 4.674  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1281 bp, 427 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 543 bp, 181 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dgk]]'', ''[[yaaI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaH]]'', ''[[yaaJ]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00160 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00160 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00160 DNA_with_flanks]
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00170 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00170 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00170 DNA_with_flanks]
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaH_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaI_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=yaaH_23868_25151_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaH_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00160]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaI_25221_25766_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yaaI_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00170]]
 
|-
 
|-
 
|}
 
|}
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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|[[sporulation proteins]]}},
+
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}}
−
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[SigB regulon]]}},
+
{{SubtiWiki regulon|[[SigB regulon]]}}
−
{{SubtiWiki regulon|[[SigE regulon]]}},
 
−
{{SubtiWiki regulon|[[SpoIIID regulon]]}}
 
  
 
=The gene=
 
=The gene=
Line 50: Line 51:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00160
+
* '''Locus tag:''' BSU00170
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaH.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10080]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10081]
  
 
=== Additional information===
 
=== Additional information===
 +
 +
  
  
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* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''[[Localization]]:'''  
+
* '''[[Localization]]:'''
−
** inner spore coat, localization depends on [[SafA]] {{PubMed|19933362,22171814}}
 
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37531 P37531]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37532 P37532]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00160]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00170]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=== Additional information===
 
=== Additional information===
  
−
required for survival of ethanol stress [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
+
important for survival of ethanol stress [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''yaaH'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed]
+
* '''Operon:'''  
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaH_23868_25151_-1 yaaH] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yaaI_25221_25766_-1 yaaI] {{PubMed|22383849}}
  
−
* '''[[Sigma factor]]:''' [[SigE]] {{PubMed|15699190,10419957}}, [[SigB]] {{PubMed|15805528}}
+
* '''Sigma factor:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
  
−
* '''Regulation:'''   
+
* '''Regulation:'''  induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
 
−
** expressed during sporulation in the mother cell ([[SigE]], [[SpoIIID]]) {{PubMed|15383836,10419957}}
 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
−
** [[SpoIIID]]: transcription repression {{PubMed|15383836}}
 
  
−
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>19087206,12884008,10419957,15805528 11964120, 19933362 22171814 15383836 22343356 18835992 </pubmed>
+
<pubmed>15805528 15805528, </pubmed>
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:54, 11 November 2013

  • Description: general stress protein, similar to isochorismatase

Gene name yaaI
Synonyms
Essential no
Product unknown
Function survival of ethanol stress
Gene expression levels in SubtiExpress: yaaI
MW, pI 20 kDa, 4.674
Gene length, protein length 543 bp, 181 aa
Immediate neighbours yaaH, yaaJ
Sequences Protein DNA DNA_with_flanks
Genetic context
YaaI context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
YaaI expression.png
























Categories containing this gene/protein

poorly characterized/ putative enzymes

This gene is a member of the following regulons

SigB regulon

The gene

Basic information

  • Locus tag: BSU00170

Phenotypes of a mutant

Database entries

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

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: [2]
  • E.C. number:

Additional information

important for survival of ethanol stress PubMed

Expression and regulation

  • Operon:
  • 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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