BBa_K1088008 1 BBa_K1088008 B. subtilis dxs-GFP fusion (lac promoter without lac inhibitor: IPTG uninducible) 2013-08-19T11:00:00Z 2015-05-08T01:09:06Z The parts mainly derive from E. coli K-12 MG1655 but the GFP as an exception comes from Aequorea victoria This composite part consists of 5 parts A lac promoter: BBa_R0010 A strong RBS: BBa_J15001 The Dxs from B. subtilis: BBa_K1088000 A 10 aa protein linker: BBa_K105012 A GFP reporter protein: BBa_E0040 false false _1398_ 0 12807 9 It's complicated false The system was assembled with USER cloning but we inserted a scar site between the RBS and start codon aswell as between the promoter and the RBS. We did this to improbe translational efficiency. We used the terminator in the pSB1C3 plasmid. false Andreas Kj??r component2373765 1 BBa_K1088000 component2373768 1 BBa_E0040 component2373766 1 BBa_K105012 component2373760 1 BBa_K1088021 component2373763 1 BBa_J15001 component2373753 1 BBa_R0010 annotation2373763 1 BBa_J15001 range2373763 1 207 216 annotation2373766 1 BBa_K105012 range2373766 1 2119 2148 annotation2373760 1 BBa_K1088021 range2373760 1 201 206 annotation2373765 1 BBa_K1088000 range2373765 1 217 2118 annotation2373753 1 BBa_R0010 range2373753 1 1 200 annotation2373768 1 BBa_E0040 range2373768 1 2149 2868 BBa_E0040 1 GFP green fluorescent protein derived from jellyfish Aequeora victoria wild-type GFP (SwissProt: P42212 2004-09-29T11:00:00Z 2016-01-26T02:09:38Z Released HQ 2013 GFP (mut3b) [note that this part does not have a barcode] false true _11_1_ 4206 61 7 In stock false true jcbraff annotation1934520 1 GFP protein range1934520 1 1 720 BBa_K1088021 1 BBa_K1088021 Mixed site (ACTAGA) 2013-09-16T11:00:00Z 2015-05-08T01:09:06Z Restriction sites Mixed site (ACTAGA)when XbaI and SpeI sticky ends ligate false false _1398_ 0 17057 9 Not in stock false None false Patrick Rosendahl Andreassen BBa_K1088000 1 dxs (B. su 1-deoxyxylulose-5-phosphate synthase (Dxs) enzyme from MEP pathway isolated from B. subtilis 168 2013-07-08T11:00:00Z 2015-05-08T01:09:06Z B. subtilis 168 The MEP pathway is a common bacterial isoprenoid pathway. To improve the yield of the end product, isopentenyl diphosphate (IPP) and dimethylallyl pyrophosphate(DMAPP), Zhao et al. expressed, in 2011, the 1-deoxyxylulose-5-phosphate synthase(Dxs)gene aswell as the second step of the MEP pathway. They saw a 2.3 fold increase in isoprene output (isoprene is one of many products from the MEP pathway). From Biocyc: "Dxs catalyzes the thiamin diphosphate-dependent reaction that condenses pyruvate and D-glyceraldehyde-3-phosphate to yield 1-deoxy-D-xylulose 5-phosphate [Julsing07]. This is the first, rate-limiting step in the methylerythritol phosphate pathway of isoprenoid biosynthesis, and is believed to feed into the pyridoxal 5-phosphate (vitamin B6) and thiamin (vitamin B1) biosynthesis pathways." -http://biocyc.org/BSUB/NEW-IMAGE?type=ENZYME&object=BSU24270-MONOMER false false _1398_ 0 12807 9 It's complicated false we changed TTG start codon to ATG to improve translation efficiency. We performed 4 silent site directed mutageneses to remove 2 EcoR1 and 2 Pst1 restriction sites false Andreas Kj??r annotation2331286 1 Dxs B. sub coding region range2331286 1 1 1901 BBa_K105012 1 BBa_K105012 10 aa flexible protein domain linker 2008-10-18T11:00:00Z 2015-05-08T01:08:52Z Oligos with a yeast optimized coding for the peptide GENLYFQSGG have been ordered <br\n> The amino acide sequence corresponds to the interdomaine linker of xxx. ''paper'' This is a 10 amino acides long linker peptide which can be used to join protein domains together in a flexible way. So fusion proteins with variable DNA-binding and activation or repression domains might be assembled. <br\n> false true _253_ 0 3313 9 In stock true To enable the fusion with other domains in frame the vector of this BioBrick has no base pair in between the restriction side and the BioBrick. Furthermore, this coding sequence does not include a start codon.<br\n> For more information about this issus, see:<br\n> Phillips, I.E. and Silver, P.A. "A new Biobrick Assembly Strategy Designed for Facile Protein Engineering." <br\n> DSpace http://hdl.handle.net/1721.1/32535 (2006). true Manuel Gersbacher, Katja Karstens BBa_R0010 1 LacI promoter (lacI regulated) 2003-01-31T12:00:00Z 2015-05-08T01:14:14Z The Plac insert was PCR'd from the MG1655 strain of E.coli K12. Released HQ 2013 Inverting regulatory region controlled by LacI (<bb_part>BBa_C0010</bb_part>, <bb_part>BBa_C0011</bb_part>, etc.) <p> The pLac regulatory region is a 243 base-pair sequence with standard BioBrick prefix and suffix sections on its ends. It contains two protein binding sites: CAP, which is generally present in E.coli and is assocciated with cell health and availability of glucose., and LacI, the Lac inhibitor <bb_part>BBa_C0010</bb_part> which binds in an dimerized cooperative manner to inhibit the transcription of the protein that follows. In the presence of lactose or IPTG, an analog of lactose, LacI is unable to correctly bind and inhibit transcription. This allows <bb_part>BBa_R0010</bb_part> to be used as a inverter or as a detector of lactose or IPTG. false true _1_ 0 24 7 In stock false <P> <P><P> LacI binds to this regulator. This part is incompatible with species containing active LacI coding regions. Lactose and IPTG disable the operation of LacI and this regulator. This part is incompatible with environments containing lactose or lactose analogs. true annotation1961223 1 CAP binding site range1961223 1 89 126 annotation1961224 1 -35 range1961224 1 137 142 annotation1961227 1 start range1961227 1 173 173 annotation1961225 1 -10 range1961225 1 161 166 annotation1961222 1 BBa_R0010 range1961222 1 1 200 annotation1961226 1 LacI binding site range1961226 1 166 200 annotation1961221 1 end of LacI coding region (inactive) range1961221 1 1 88 BBa_J15001 1 BBa_J15001 strong synthetic E. coli ribosome binding site with SacI site. 2007-07-12T11:00:00Z 2015-08-31T04:08:32Z Synthetic. This is a strong synthetic E. coli ribosome binding site. It is synthesised as two complementary oligonucleotides rather than being incorporated into a biobrick plasmid. It incorporates a SacI site overlapping the XbaI site, which is preserved when it is added to any other biobrick. This allows easy detection of the RBS after it has been added upstream of a biobrick coding sequence in a plasmid vector. false false _163_ 0 837 163 Not in stock false Note the presence of a SacI site overlapping the XbaI site, which is preserved when this biobrick is added to any other biobrick. At the time of writing, this biobrick is added as a short piece of DNA composed of two complementary oligonucleotides rather than being incorporated into a biobrick cloning vector by itself. It can be added upstream of a biobrick coding sequence, and its presence can easily be detected in miniprep DNA on a gel by using a SacI-SpeI or similar digest. false Chris French annotation1938045 1 SacI range1938045 1 1 3 annotation1938046 1 rbs range1938046 1 4 10 BBa_K1088008_sequence 1 caatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacacaactagactcaaggaggatggatcttttatcaatacaggacccgtcgtttttaaaaaacatgtccattgatgaattagagaaattaagtgatgaaatccgtcagtttttaattacaagtttatccgcttccggcggccacatcggcccaaacttaggtgtcgtagagcttactgttgccctgcataaggaatttaacagcccgaaagacaaatttttatgggatgtaggccatcagtcgtatgtccataagctgctgacaggacgcggaaaagaatttgcgacgcttcgccagtacaaagggctttgcggatttccaaagcggagtgaaagcgagcacgatgtttgggaaaccgggcacagctcgacttctctgtcaggcgcgatgggaatggcagctgcccgtgatattaaaggaacggatgaatatattattccgatcattggtgacggcgcgctgaccggcggtatggcgctcgaagcccttaaccacatcggcgacgagaaaaaagacatgattgtcatccttaatgataatgaaatgagtattgcgccaaacgtcggtgccattcactctatgctcggacggctccgcactgcggggaaataccagtgggtcaaagatgagcttgaatacttatttaaaaagattccggcagttgggggcaagcttgccgccacggcggaacgggtcaaagacagcctgaaatacatgctcgtctccggaatgtttttcgaggagctcggttttacgtatttgggcccagtggacggacattcttatcatgagctgattgagaatcttcaatacgccaaaaaaacgaaaggccctgttcttctgcacgtcattacgaaaaaagggaaggggtacaaaccggctgagaccgatacgattgggacatggcatggtaccggaccatataaaattaataccggtgactttgtaaagccgaaagccgcagctccttcgtggagcggtcttgtcagcggaactgtgcagcgaatggcgcgcgaggacggacgcattgtagccattacgccggctatgcctgtcggttcaaagcttgaaggcttcgcaaaggaattccctgaccggatgttcgacgtaggaatcgcagaacagcatgccgcaacaatggctgcagctatggcaatgcagggtatgaagccgtttttggcgatttactcaaccttcctgcaaagggcatatgaccaagttgttcatgacatctgccgccaaaacgctaatgtgtttattggaattgaccgtgctggactcgttggcgctgatggagagacacatcaaggcgtgtttgatattgcgtttatgcgccacattccaaacatggtcttaatgatgccgaaagacgaaaatgaaggccagcacatggttcatacagcacttagctatgacgaaggcccgatagcaatgcgttttccgcgcggaaacggactcggcgtaaaaatggatgaacagttgaaaacgattccgatcggtacgtgggaggtgctgcgtccagggaacgatgctgtcatcttaacattcggcacaacaatcgaaatggcgattgaagcagccgaagagctgcagaaagaaggcctttccgtgcgcgttgtgaatgcgcgttttattaagccgattgatgaaaagatgatgaagagtatcctaaaagaaggcttgccaattttaacaattgaagaagcggtcttagaaggcggtttcggaagctcgattttagaattcgctcatgatcaaggtgaatatcatactccgattgacagaatgggtatacctgatcggtttattgaacacggaagtgtaacagcgcttcttgaggaaattggactgacaaaacagcaggtggcaaatcgtattagattactgatgccaccaaagacacacaaaggaattggatcatgaggtgaaaatttgtattttcaatctggtggtatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa BBa_R0010_sequence 1 caatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggcaccccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggataacaatttcacaca BBa_J15001_sequence 1 ctcaaggagg BBa_K1088000_sequence 1 atggatcttttatcaatacaggacccgtcgtttttaaaaaacatgtccattgatgaattagagaaattaagtgatgaaatccgtcagtttttaattacaagtttatccgcttccggcggccacatcggcccaaacttaggtgtcgtagagcttactgttgccctgcataaggaatttaacagcccgaaagacaaatttttatgggatgtaggccatcagtcgtatgtccataagctgctgacaggacgcggaaaagaatttgcgacgcttcgccagtacaaagggctttgcggatttccaaagcggagtgaaagcgagcacgatgtttgggaaaccgggcacagctcgacttctctgtcaggcgcgatgggaatggcagctgcccgtgatattaaaggaacggatgaatatattattccgatcattggtgacggcgcgctgaccggcggtatggcgctcgaagcccttaaccacatcggcgacgagaaaaaagacatgattgtcatccttaatgataatgaaatgagtattgcgccaaacgtcggtgccattcactctatgctcggacggctccgcactgcggggaaataccagtgggtcaaagatgagcttgaatacttatttaaaaagattccggcagttgggggcaagcttgccgccacggcggaacgggtcaaagacagcctgaaatacatgctcgtctccggaatgtttttcgaggagctcggttttacgtatttgggcccagtggacggacattcttatcatgagctgattgagaatcttcaatacgccaaaaaaacgaaaggccctgttcttctgcacgtcattacgaaaaaagggaaggggtacaaaccggctgagaccgatacgattgggacatggcatggtaccggaccatataaaattaataccggtgactttgtaaagccgaaagccgcagctccttcgtggagcggtcttgtcagcggaactgtgcagcgaatggcgcgcgaggacggacgcattgtagccattacgccggctatgcctgtcggttcaaagcttgaaggcttcgcaaaggaattccctgaccggatgttcgacgtaggaatcgcagaacagcatgccgcaacaatggctgcagctatggcaatgcagggtatgaagccgtttttggcgatttactcaaccttcctgcaaagggcatatgaccaagttgttcatgacatctgccgccaaaacgctaatgtgtttattggaattgaccgtgctggactcgttggcgctgatggagagacacatcaaggcgtgtttgatattgcgtttatgcgccacattccaaacatggtcttaatgatgccgaaagacgaaaatgaaggccagcacatggttcatacagcacttagctatgacgaaggcccgatagcaatgcgttttccgcgcggaaacggactcggcgtaaaaatggatgaacagttgaaaacgattccgatcggtacgtgggaggtgctgcgtccagggaacgatgctgtcatcttaacattcggcacaacaatcgaaatggcgattgaagcagccgaagagctgcagaaagaaggcctttccgtgcgcgttgtgaatgcgcgttttattaagccgattgatgaaaagatgatgaagagtatcctaaaagaaggcttgccaattttaacaattgaagaagcggtcttagaaggcggtttcggaagctcgattttagaattcgctcatgatcaaggtgaatatcatactccgattgacagaatgggtatacctgatcggtttattgaacacggaagtgtaacagcgcttcttgaggaaattggactgacaaaacagcaggtggcaaatcgtattagattactgatgccaccaaagacacacaaaggaattggatcatga BBa_E0040_sequence 1 atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa BBa_K1088021_sequence 1 actaga BBa_K105012_sequence 1 ggtgaaaatttgtattttcaatctggtggt igem2sbol 1 iGEM to SBOL conversion Conversion of the iGEM parts registry to SBOL2.1 James Alastair McLaughlin Chris J. Myers 2017-03-06T15:00:00.000Z