Difference between revisions of "Sandbox"
| Line 1: | Line 1: | ||
| − | * '''Description:''' | + | * '''Description:''' unknown function <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''' | ||
| − | |'' | + | |''ymdB'' |
|- | |- | ||
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' '' | |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''' || | + | |style="background:#ABCDEF;" align="center"| '''Product''' || YmdB protein |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Function''' || | + | |style="background:#ABCDEF;" align="center"|'''Function''' || unknown function |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || | + | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29,1 kDa, 6.50 |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 amino acids |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rny]]'', ''[[spoVS]]'' |
|- | |- | ||
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein''' | |colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein''' | ||
|- | |- | ||
| − | + | |colspan="2" | '''Genetic context''' <br/> [[Image:ymdB_context.gif]] | |
| − | |||
| − | |colspan="2" | '''Genetic context''' <br/> [[Image: | ||
<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 37: | Line 35: | ||
=== Basic information === | === Basic information === | ||
| − | * '''Coordinates:''' | + | * '''Coordinates:''' 1768211 - 1769002 |
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
| + | |||
| + | strong overexpression of [[Hag]] | ||
=== Database entries === | === Database entries === | ||
| − | * '''DBTBS entry:''' | + | * '''DBTBS entry:''' no entry |
| − | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+ | + | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13421] |
=== Additional information=== | === Additional information=== | ||
| − | |||
=The protein= | =The protein= | ||
| Line 54: | Line 53: | ||
=== Basic information/ Evolution === | === Basic information/ Evolution === | ||
| − | * '''Catalyzed reaction/ biological activity:''' | + | * '''Catalyzed reaction/ biological activity:''' negative effector of the expression of ''[[hag]]'' and other members of the [[SigD]] regulon |
* '''Protein family:''' | * '''Protein family:''' | ||
| − | * '''Paralogous protein(s):''' | + | * '''Paralogous protein(s):''' similar to unknown proteins |
=== Extended information on the protein === | === Extended information on the protein === | ||
| Line 74: | Line 73: | ||
* '''Interactions:''' | * '''Interactions:''' | ||
| − | * '''Localization:''' | + | * '''Localization:''' |
=== Database entries === | === Database entries === | ||
| Line 80: | Line 79: | ||
* '''Structure:''' | * '''Structure:''' | ||
| − | * '''Swiss prot entry:''' | + | * '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31775] |
| − | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+ | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16970] |
* '''E.C. number:''' | * '''E.C. number:''' | ||
=== Additional information=== | === Additional information=== | ||
| + | has a negative effect on ''[[hag]]'' expression | ||
=Expression and regulation= | =Expression and regulation= | ||
| − | * '''Operon:''' | + | * '''Operon:''' ''[[rny]]-[[ymdB]]'' |
| − | * ''' | + | * '''Sigma factor:''' |
| − | * '''Regulation:''' | + | * '''Regulation:''' constitutive |
* '''Regulatory mechanism:''' | * '''Regulatory mechanism:''' | ||
| − | * '''Additional information:''' | + | * '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there |
=Biological materials = | =Biological materials = | ||
| − | * '''Mutant:''' | + | * '''Mutant:''' GP583 (spc), available in [[Stülke]] lab |
| − | * '''Expression vector:''' | + | * '''Expression vector:''' pGP1040 (N-terminal His-tag, in [[pWH844]]), pGP1041 (N-terminal Strep-tag, for SPINE, expression in ''B. subtilis'', in [[pGP380]]), available in [[Stülke]] lab |
| − | + | ||
* '''lacZ fusion:''' | * '''lacZ fusion:''' | ||
* '''GFP fusion:''' | * '''GFP fusion:''' | ||
| − | * '''two-hybrid system:''' | + | * '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab |
* '''Antibody:''' | * '''Antibody:''' | ||
=Labs working on this gene/protein= | =Labs working on this gene/protein= | ||
| + | |||
| + | [[Stülke|Jörg Stülke]], University of Göttingen, Germany | ||
| + | [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage] | ||
=Your additional remarks= | =Your additional remarks= | ||
| Line 120: | Line 123: | ||
=References= | =References= | ||
| − | |||
# 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 15:23, 15 April 2009
- Description: unknown function
| Gene name | ymdB |
| Synonyms | |
| Essential | no |
| Product | YmdB protein |
| Function | unknown function |
| MW, pI | 29,1 kDa, 6.50 |
| Gene length, protein length | 792 bp, 264 amino acids |
| Immediate neighbours | rny, spoVS |
| Hier soll was neues rein | |
Genetic context 
This image was kindly provided by SubtiList
| |
Contents
The gene
Basic information
- Coordinates: 1768211 - 1769002
Phenotypes of a mutant
strong overexpression of Hag
Database entries
- DBTBS entry: no entry
- SubtiList entry: [1]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity: negative effector of the expression of hag and other members of the SigD regulon
- Protein family:
- Paralogous protein(s): similar to unknown proteins
Extended information on the protein
- Kinetic information:
- Domains:
- Modification:
- Cofactor(s):
- Effectors of protein activity:
- Interactions:
- Localization:
Database entries
- Structure:
- Swiss prot entry: [2]
- KEGG entry: [3]
- E.C. number:
Additional information
has a negative effect on hag expression
Expression and regulation
- Sigma factor:
- Regulation: constitutive
- Regulatory mechanism:
- Additional information: there is a terminator between rny and ymdB, most transcripts terminate there
Biological materials
- Mutant: GP583 (spc), available in Stülke lab
- Expression vector: pGP1040 (N-terminal His-tag, in pWH844), pGP1041 (N-terminal Strep-tag, for SPINE, expression in B. subtilis, in pGP380), available in Stülke lab
- lacZ fusion:
- GFP fusion:
- two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
- Antibody:
Labs working on this gene/protein
Jörg Stülke, University of Göttingen, Germany Homepage
Your additional remarks
References
- Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
