Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' similar to ribosomal protein S1 <br/><br/>
+
* '''Description:''' assembly of the 50S subunit of the ribosome <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'''
−
|''ypfD''
+
|''yphC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''jofD ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' engA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || GTPase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || assembly of the 50S subunit of the ribosome
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 4.569  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.248  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1146 bp, 382 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1308 bp, 436 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fni]]'', ''[[cmk]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gpsA]]'', ''[[seaA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14204&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14200&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ypfD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yphC_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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU22880
+
* '''Locus tag:''' BSU22840
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: Line 45:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11005]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11443]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Binds and hydrolyzes GTP and readily exchanges GDP for GTP
  
−
* '''Protein family:''' ribosomal protein S1P family (according to Swiss-Prot)
+
* '''Protein family:''' EngA subfamily (according to Swiss-Prot) Era/Obg family
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[Era]], [[Obg]], [[YphC]], [[YsxC]], [[RbgA]], [[YqeH]], [[ThdF]], [[YyaF]], [[YnbA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 64: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser-243 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 76: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2HJG 2HJG] (complex with GDP)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P38494 P38494]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P50743 P50743]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU22880]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU22840]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 113: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Naotake Ogasawara]], Nara, Japan
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 122:
 
=References=
 
=References=
  
−
<pubmed>17218307, </pubmed>
+
<pubmed>12427945, </pubmed>
−
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
+
# Morimoto T, Loh PC, Hirai T, Asai K, Kobayashi K, Moriya S, Ogasawara N (2002) Six GTP-binding proteins of the Era/Obg family are essential for cell growth in ''Bacillus subtilis''. ''Microbiology'' '''148:''' 3539-3552. [http://www.ncbi.nlm.nih.gov/sites/entrez/12427945 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:48, 8 June 2009

  • Description: assembly of the 50S subunit of the ribosome

Gene name yphC
Synonyms engA
Essential yes PubMed
Product GTPase
Function assembly of the 50S subunit of the ribosome
MW, pI 48 kDa, 5.248
Gene length, protein length 1308 bp, 436 aa
Immediate neighbours gpsA, seaA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YphC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU22840

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Binds and hydrolyzes GTP and readily exchanges GDP for GTP
  • Protein family: EngA subfamily (according to Swiss-Prot) Era/Obg family

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure: 2HJG (complex with GDP)
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Naotake Ogasawara, Nara, Japan

Your additional remarks

References

Takuya Morimoto, Pek Chin Loh, Tomohiro Hirai, Kei Asai, Kazuo Kobayashi, Shigeki Moriya, Naotake Ogasawara
Six GTP-binding proteins of the Era/Obg family are essential for cell growth in Bacillus subtilis.
Microbiology (Reading): 2002, 148(Pt 11);3539-3552
[PubMed:12427945] [WorldCat.org] [DOI] (P p)

  1. Morimoto T, Loh PC, Hirai T, Asai K, Kobayashi K, Moriya S, Ogasawara N (2002) Six GTP-binding proteins of the Era/Obg family are essential for cell growth in Bacillus subtilis. Microbiology 148: 3539-3552. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=89020"