Difference between revisions of "Sandbox"
| Line 1: | Line 1: | ||
| − | * '''Description:''' | + | * '''Description:''' RNA polymerase [[sigma factor]] SigD <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''' | ||
| − | |'' | + | |''sigD'' |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''flaB '' |
|- | |- | ||
|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''' || RNA polymerase [[sigma factor]] SigD |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Function''' || motility, chemotaxis | + | |style="background:#ABCDEF;" align="center"|'''Function''' || regulation of flagella, motility, chemotaxis and autolysis |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || | + | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.167 |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa |
|- | |- | ||
| − | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cheD]]'', ''[[swrB]]'' |
|- | |- | ||
| − | |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS: | + | |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13520]+-newId sequences] <br/> (Barbe ''et al.'', 2009)''' |
|- | |- | ||
| − | |colspan="2" | '''Genetic context''' <br/> [[Image: | + | |colspan="2" | '''Genetic context''' <br/> [[Image:sigD_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 43: | Line 43: | ||
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html] | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html] | ||
| − | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+ | + | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10751] |
=== Additional information=== | === Additional information=== | ||
| Line 57: | Line 57: | ||
* '''Paralogous protein(s):''' | * '''Paralogous protein(s):''' | ||
| + | |||
| + | === Genes/ operons controlled by SigD === | ||
| + | ''[[dltA]]-[[dltB]]-[[dltC]]-[[dltD]]-[[dltE]]'', ''[[cheV]]'', ''[[degR]]'', ''[[epr]]'', ''[[hag]]'', ''[[lytA]]-[[lytB]]-[[lytC]]'', ''[[lytD]]'', ''[[lytF]]'', ''[[tlpA]]-[[mcpA]]'', ''[[mcpB]]'', ''[[mcpC]]'', ''[[motA]]-[[motB]]'', ''[[nfrA]]-[[ywcH]]'' | ||
=== Extended information on the protein === | === Extended information on the protein === | ||
| Line 70: | Line 73: | ||
* '''Effectors of protein activity:''' | * '''Effectors of protein activity:''' | ||
| − | * '''Interactions:''' [[ | + | * '''Interactions:''' [[SigD]]-[[FlgM]], |
* '''Localization:''' | * '''Localization:''' | ||
| Line 80: | Line 83: | ||
* '''Swiss prot entry:''' | * '''Swiss prot entry:''' | ||
| − | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+ | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16470] |
* '''E.C. number:''' | * '''E.C. number:''' | ||
| Line 90: | Line 93: | ||
* '''Operon:''' | * '''Operon:''' | ||
| − | * '''[[Sigma factor]]:''' | + | * '''[[Sigma factor]]:''' |
* '''Regulation:''' | * '''Regulation:''' | ||
| Line 96: | Line 99: | ||
* '''Regulatory mechanism:''' | * '''Regulatory mechanism:''' | ||
| − | * '''Additional information:''' | + | * '''Additional information:''' |
=Biological materials = | =Biological materials = | ||
| Line 108: | Line 111: | ||
* '''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:''' | ||
Revision as of 23:04, 27 April 2009
- Description: RNA polymerase sigma factor SigD
| Gene name | sigD |
| Synonyms | flaB |
| Essential | no |
| Product | RNA polymerase sigma factor SigD |
| Function | regulation of flagella, motility, chemotaxis and autolysis |
| MW, pI | 29 kDa, 5.167 |
| Gene length, protein length | 762 bp, 254 aa |
| Immediate neighbours | cheD, swrB |
| Get the DNA and protein sequences (Barbe et al., 2009) | |
Genetic context 
This image was kindly provided by SubtiList
| |
Contents
The gene
Basic information
- Coordinates:
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):
Genes/ operons controlled by SigD
dltA-dltB-dltC-dltD-dltE, cheV, degR, epr, hag, lytA-lytB-lytC, lytD, lytF, tlpA-mcpA, mcpB, mcpC, motA-motB, nfrA-ywcH
Extended information on the protein
- Kinetic information:
- Domains:
- Modification:
- Cofactor(s):
- Effectors of protein activity:
- Localization:
Database entries
- Structure:
- Swiss prot entry:
- KEGG entry: [3]
- 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: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
- Antibody:
Labs working on this gene/protein
Your additional remarks
References
- Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
