IGEM:IMPERIAL/2008/Sequence: Difference between revisions
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| 3.Gene|| sinR || [http://openwetware.org/wiki/Image:SinR.doc Protein]<br> [http://openwetware.org/wiki/Image:SinR_biobrick.doc Biobrick] || [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene NCBI GENE] || QQ, J, C <font color=green> J- Changed the start codon to ATG for optimisation, needs double checking again</font>||377 | | 3.Gene|| sinR || [http://openwetware.org/wiki/Image:SinR.doc Protein]<br> [http://openwetware.org/wiki/Image:SinR_biobrick.doc Biobrick] || [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene NCBI GENE] || QQ, J, C <font color=green> J- Changed the start codon to ATG for optimisation, needs double checking again</font>||377 | ||
|- | |- | ||
| 4.Gene||XylR || | | 4.Gene||XylR || [http://openwetware.org/wiki/Image:XylR_Gene_Biorbick.doc XylR Gene Biobrick] || [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene NCBI GENE] || C || 1094 | ||
|- | |- | ||
| 5. Gene||LacI|| [http://partsregistry.org/wiki/index.php?title=Part:BBa_C0012 BBa_C0012] | | 5. Gene||LacI|| [http://partsregistry.org/wiki/index.php?title=Part:BBa_C0012 BBa_C0012] | ||
Revision as of 09:02, 30 July 2008
Hello Team Sequence, Thought we could use this page to load up all the information. If we could load up the sequence of the parts here, probably load the pure sequence then one with the restriction sites on the end. Here are some useful websites about the ends:
- http://partsregistry.org/Help:BioBrick_Prefix_and_Suffix
- http://partsregistry.org/Assembly:RBS-CDS_issues
To do list
- Tom - Find transcription terminators for B.subtilis, Two papers to start with are here
- Finish triple check
- Chris - How were the RBS derived? - By locating the sequence between gene and promoter on NCBI sequence viewer
- Get sequence for LacI -> Registry part found: BBa_C0012 [1]
- Get sequence for xylR if needed Sequence found
- Choose parts we want to use
- Work out assembly
Parts
| Part Class | Part Name | Sequence File | Papers/References | Checked | Biobrick Length (bp) |
| Promoter | |||||
| 1.Promoter - Light | Pctc | Pctc Biobrick |
Paper DBTBS | J, QQ, C | 99bp |
| 2.Promoter - σB | PgsiB | PgsiB Biobrick |
Paper DBTBS | J, C, QQ | 81bp |
| 3.Promoter - ComK upregulated | PcomC | PcomC Biobrick |
DBTBS Paper | C, J, QQ | 137bp |
| 4.Promoter - Constitutuive | P43 | P43 Biobrick |
Paper Paper2 |
C, J, QQ | 99bp |
| 5.Promoter - Inducible | Phyper-spank | Ph-s Biobrick |
Dr. Angelika Grundling (Imperial College London), Dr. Jan-Willem Veening (Newcastle University), Paper1, Paper2, Paper3, NEBcutter2 | C, J, QQ | 145bp |
| 6.Promoter - Inducible | Pxyl | Pxyl Biobrick |
Dr. Jan-Willem Veening (Newcastle University), DBTBS, Paper1, Paper2 | C, J | 125bp |
| 7.Promoter - Contitutive (high) | Pveg | Pveg Biobrick |
Dr. Jan-Willem Veening (Newcastle University), DBTBS | C, J, QQ | 87 |
| RBS | |||||
| 1.RBS | RBS-gsiB | Alt RBS Biobrick | Alt paper reference | J, QQ, C | 57 |
| 2.RBS | RBS-ctc | Biobrick | Alt paper reference | J, C, QQ | 51 |
| 3.RBS | RBS-SpoVG | RBS-spoVG Alt Biobrick | Paper | J, C, QQ | 55 |
| Gene | |||||
| 1.Gene | epsE | Protein Biobrick |
Page 9, Online Supplementary Material for "A Molecular Clutch Disables Flagella in the Bacillus subtilis Biofilm" | QQ, J, C | 878 |
| 2.Gene | ytvA | Protein Biobrick |
Partial sequence (LOV domain) | QQ, J, C | 786 |
| 3.Gene | sinR | Protein Biobrick |
NCBI GENE | QQ, J, C J- Changed the start codon to ATG for optimisation, needs double checking again | 377 |
| 4.Gene | XylR | XylR Gene Biobrick | NCBI GENE | C | 1094 |
| 5. Gene | LacI | BBa_C0012 | |||
| 6.Biomaterial | EP24-20-20 | Biobrick | Paper | QQ, J, C needs codon usage modification for B.subtilis and Need to resolve issue of signal peptide and biomaterial | 640 |
| 7.Biomaterial | EAK16-II | Biobrick | Paper | QQ, J, C Need to resolve issue of signal peptide and biomaterial | 92 |
| 8.Signal Peptide | SacB | Biobrick | Paper for signal peptide | QQ, C Wrong - See below | 139 |
| 9.Signal Peptide | LipA | Biobrick | Paper for signal peptide | QQ, C The prefix is wrong check out the second of the links i posted at the top of the page | 145 |
| 10.Signal Peptide | Epr | Biobrick | Paper for signal peptide | QQ, C, J- Wrong - See above | 133 |
| Terminator |
More improtantly, the B.subtilis RBS appears to be a 9bp sequence complementary to the a section of the 16S rRNA (3' end) from the 30S ribosome small subunit.[1] It is indicated that this may be due to a lack of the S1 protein in the B.subtilis ribosome.[2]. The complementary sequence is 5'-AAGGAGGTG-3'
As such, any sequence with high homology to this sequence may be used, in particular,Thorsted et al. (1999)[3] identified several putative RBSs in a B.subtilis vector that have reasonable homology. It may also be possible to simply use the complementary sequence to use as our RBS.
- 11 pmid=9678589
- 12 pmid=3937526
- 13 pmid=10366533
The Parts Grave Yard
For those parts that never made, rest in peace!!
| Part Class | Part Name | Sequence File | Papers/References | Reason Scrapped | Biobrick Length (bp) |
| Terminator | |||||
| 1.Terminator | TermI-VI Consensus of 6 terminators |
6NSCT Protein Biobrick |
Search for additional replication terminators in the Bacillus subtilis chromosome | For rep not scrip - BRB, killing self ~ Tom Adie 09:41, 30 July 2008 (UTC) | 30bp |
| 2.Terminator | rrnO | rrnO Biobrick | Dr. Jan-Willem Veening (Newcastle University) | Too Long | 133bp (with extra frame-shift base) |
| 3.Terminator | rrnA | rrnA Biobrick | Dr. Jan-Willem Veening (Newcastle University) | Too Long | 132bp (with extra frame-shift base) |
| RBS | |||||
| 2.RBS - Strong | RBS-spoVG | RBS-spoVG Biobrick |
Paper (reference only) DBTBS | Sequence incorrect, alternate sequence correct | 68bp |
| 3.RBS - Strong | RBS-PBS | RBS-PBS Biobrick |
Dr. Jan-Willem Veening (Newcastle University), Paper | Too short | |
| 4.RBS - Strong | RBS-ctc | Biobrick | Alt paper reference | J | 57 |
