BBa_K1422500 1 BBa_K1422500 Zea mays S-adenosylmethione synthase (corn SAM synthase) 2014-10-12T11:00:00Z 2015-05-08T01:10:23Z It comes from corn and was found on the NCBI website. NCBI. (2014). S-adenosylmethionine synthetase 1 [Zea mays]. http://www.ncbi.nlm.nih.gov/protein/NP_001148708.1 S-adenosylmethione synthase (SAM synthase) alters L-methionine to have an adenosyl bonded to a sulfer on the L-methionine, producing S-adenosylmethione (SAM). This is the first enzyme in the sequence to produce corn phytosiderophores. BBa_K1422501, BBa_K1422502, and BBa_K1422503 are also required to produce a corn phytosiderophore. false false _1800_ 0 21316 9 Not in stock false This sequence is codon optimized for Bacillus subtilis (the difference being that the 368th amino acid sequence was changed to AGG). false Casey Martin BBa_K1422504 1 BBa_K1422504 Lactose-induced Killswitch using antiholin Hyb5 2014-10-16T11:00:00Z 2015-05-08T01:10:23Z Hyb5 comes from NCBI NCBI. (2 December, 2008). Lactobacillus phage YB5 holin gene, complete cds. http://www.ncbi.nlm.nih.gov/nuccore/EF623894?report=GenBank This is a killswitch designed for Bacillus subtilis. It is lactose and IPTG inducible, has a RBS that has high efficiency with Bacillus subtilis, the antiholin Hyb5 as a lysing agent, and a forward terminator. Hyb5 was chosen because it is effective on Bacillus subtilis at neutral pH and 37 Celsius. It is also effective on certain strains of E. coli and other bacteria. Source: Wang, S.; Kong, J.; & Zhang, X. (19 November, 2008). Identification and characterization of the two-component cell lysis cassette encoded by temperate bacteriophage &#981;PYB5 of Lactobacillus fermentum. Journal of Applied Microbiology, Volume 105, Issue 6, pages 1939-1944. DOI: 10.1111/j.1365-2672.2008.03953.x http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2008.03953.x/full false false _1800_ 0 21316 9 Not in stock false This killswitch is intended for Bacillus subtilis, and as such uses a RBS that works well in Bacillus. The choice of lactose as a promoter was chosen because it penetrates soil, is economically feasible to spread across a field, is not a food source for Bacillus, and does not harm plants or the natural soil microbiome. Hyb5 was chosen as a lysing agent because it is effective on Bacillus subtilis at neutral pH around field temperature. false Casey Martin annotation2429860 1 BBa_B1006 range2429860 1 5 39 annotation2429857 1 PlaC range2429857 1 2 107 annotation2429859 1 hyb5 range2429859 1 4 455 annotation2429858 1 BBa_K143021 range2429858 1 3 12 BBa_E1010 1 mRFP1 **highly** engineered mutant of red fluorescent protein from Discosoma striata (coral) 2004-07-27T11:00:00Z 2015-08-31T04:07:26Z Campbell et al., PNAS v99 p7877 <a href="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12060735">URL</a> Released HQ 2013 monomeric RFP: Red Fluorescent Protein. Excitation peak: 584 nm Emission peak: 607 nm false false _11_1_ 0 52 7 In stock false TAATAA double stop codon added (DE). Four silent mutations made to remove three EcoRI sites and one PstI site: A28G, A76G, A349G, G337A. true Drew Endy annotation1014044 1 mrfp1 range1014044 1 1 675 annotation2214014 1 Help:Barcodes range2214014 1 682 706 BBa_B1006 1 BBa_B1006 Terminator (artificial, large, %T~>90) 2006-08-30T11:00:00Z 2015-08-31T04:07:21Z modified E. coli thr terminator, replaced all A-T pairs in stem with C-G pairs Released HQ 2013 Artificial terminator, estimated %T~>90% *8bp stem, 6nt loop *Bidirectional, estimated reverse %T~>90% false true _41_ 0 745 41 In stock false Bidirectional, with the reverse estimated to be less effective than the forward. Has a polyA tail of 9 residues. true Haiyao Huang annotation1898430 1 PolyA range1898430 1 32 39 annotation1898428 1 B1006 range1898428 1 1 39 annotation1898431 1 PolyA range1898431 1 1 9 annotation1898429 1 modified thr terminator range1898429 1 10 31 BBa_K1422501 1 BBa_K1422501 Zea mays nicotianamine synthase (corn NAS) 2014-10-12T11:00:00Z 2015-05-08T01:10:23Z The original sequence came from the NCBI website. NCBI. (5 February, 2003). Zea mays ZmNAS1 mRNA, complete cds. http://www.ncbi.nlm.nih.gov/nuccore/19911063 Nicotianamine synthase (NAS) catalyzes the trimerization of SAM molecules to form nicotianamine (NA). It is the second enzyme of four used to produce corn phytosiderophores. BBa_K1422500, BBa_K1422502, and BBa_K1422503 are also needed to produce a phytosiderophore. false false _1800_ 0 21316 9 Not in stock false Codon optimized for Bacillus subtilis. The 28th, 115th, and 140th amino acid sequences were changed to CTA from CTT. false Casey Martin BBa_K143021 1 RBS-spoVG SpoVG ribosome binding site (RBS) for B. subtilis 2008-09-16T11:00:00Z 2015-05-08T01:10:23Z The sequence was taken from a previous research paper [1] and was constructed by Geneart. Released HQ 2013 Description: SpoVG is an endogenous ribosome binding site from B.subtilis. The sequence of the spoVG ribosome binding site is AAAGGUGGUGA which is complementary to the sequence UUUCCUCCACU from the 3' region of the 16s rRNA from B.subtilis. Previous research showed that the predicted binding energy of the 16s rRNA to the RBS is -19kcal <cite>1</cite> false true _199_ 0 2090 9 In stock false In order to ensure that the RBS is functional the actual ribosome binding site was maintained and the distance between the RBS and the start codon maintained. In order to conform to the biobrick standard the sequence flanking the RBS had to be changed but the distance between the promoter and RBS, and start codon and RBS was maintained. false James Chappell annotation1975997 1 rbs range1975997 1 1 12 BBa_K1422505 1 BBa_K1422505 Lactose-inducible killswitch, produces SAMS and NAS1 2014-10-16T11:00:00Z 2015-05-08T01:10:23Z Many of the genes (Hyb5, SAMS, and NAS1) come fromNCBI. (2 December, 2008). Lactobacillus phage YB5 holin gene, complete cds. http://www.ncbi.nlm.nih.gov/nuccore/EF623894?report=GenBank NCBI. NCBI. (2014). S-adenosylmethionine synthetase 1 [Zea mays]. http://www.ncbi.nlm.nih.gov/protein/NP_001148708.1 NCBI. (5 February, 2003). Zea mays ZmNAS1 mRNA, complete cds. http://www.ncbi.nlm.nih.gov/nuccore/19911063 This plasmid includes a killswitch and produces SAMS (BBa_K1422500) and NAS1 (BBa_K1422501), two of the four enzymes used in the production of corn phytosiderophores. The killswitch (BBa_K1422504) is lactose and IPTG inducible and uses the antiholin Hyb5 to lyse the cell. The corn genes are codon optimized for Bacillus subtilis, and the RBS ("SpoVG" BBa_K143021) has shown high strength in Bacillus subtilis. mRFP is used as a reporter because it is easily observed, easily measured, and expressed in Bacillus subtilis. false false _1800_ 0 21316 9 Not in stock false The kill switch is located at the beginning of a plasmid to avoid being accidentally translated by an mRNA due to a previous section not being properly terminated. The reporter is placed after the corn genes because gene expression decreases linearly as the distance from the promoter increases, and expressing the corn genes is much more important than expressing the reporter. The corn genes are codon optimized for Bacillus subtilis (details are on their respective Registry pages). false Casey Martin component2429898 1 BBa_E1010 component2429892 1 BBa_K143021 component2429895 1 BBa_K143021 component2429890 1 BBa_K1422500 component2429884 1 BBa_K1422504 component2429887 1 BBa_K143012 component2429903 1 BBa_B1006 component2429889 1 BBa_K143021 component2429893 1 BBa_K1422501 annotation2429889 1 BBa_K143021 range2429889 1 727 738 annotation2429893 1 BBa_K1422501 range2429893 1 2103 3086 annotation2429890 1 BBa_K1422500 range2429890 1 747 2076 annotation2429895 1 BBa_K143021 range2429895 1 3095 3106 annotation2429892 1 BBa_K143021 range2429892 1 2085 2096 annotation2429903 1 BBa_B1006 range2429903 1 3827 3865 annotation2429887 1 BBa_K143012 range2429887 1 622 718 annotation2429884 1 BBa_K1422504 range2429884 1 1 613 annotation2429898 1 BBa_E1010 range2429898 1 3113 3818 BBa_K143012 1 Pveg Promoter veg a constitutive promoter for B. subtilis 2008-09-10T11:00:00Z 2015-05-08T01:10:23Z The Pveg promoter was suggested to us by Dr. Jan-Willem Veening of Newcastle University. This sequence supplied was compared to that of the DBTBS database<cite>#3</cite> then a section containing the binding site synthesised by Geneart. Released HQ 2013 Pveg is a constitutive promoter that constitutively expresses the P43 protein in ''B.subtilis''. Pveg contains binding sites for the ''B.sutbilis'' major sigma factor<cite>#1</cite>. Pveg in ''B.subtilis'' utilises two binding sites to cause high expression of genes<cite>#2</cite>, however our Pveg is lacking the upstream site to give a medium level of gene expression. It has been noted that the sporulation master regulatoion factor spoOA interacts with Pveg though it is not known how<cite>#3</cite>. The context with which we used the promoter Pveg is as a '''Polymerase Per Second''' (PoPS) generator. false true _199_ 0 2090 9 In stock false The biobrick part was designed to include a single binding site for the ''B.subtilis major sigma factor. In addition the biobrick standard was applied to the promoter Pveg sequence. false James Chappell annotation1975704 1 Sigma A-35 range1975704 1 63 68 annotation1975705 1 Sigma A -10 range1975705 1 86 91 BBa_K143021_sequence 1 aaaggtggtgaa BBa_K1422500_sequence 1 cgtgctacacacccttctccgttcgcttcttcaccgccttcttgccgtgtgttgaacaaagaacaacagcgtaaaagacttgtagaacgtgcacgccgccgtcaatggcgtcgtcgtgcttcatgcagcccaagaagtccgtgaactcgtggaacacagacaagctgtgcaacacgctgtcgcactcgctgttggacgccggcatggcgtcgcacaccgacagctagatggcctgcacgtccagcaccgcgtcgtacatggtgatggtgttctgcacgtagcccgccaagacgcgcttggacgacacgcagatcttgcgcgacaccggcagcacgttctggctcaccgccgacaacatggggatctacacctactgcagcgagatgttggtgaacctcctcatcttcacctcctacgtctcgccgcgcctgcacgggaacaagccgctccggaccacgtcgtagcgcccctgcaacacgtgccacttgcagcggaacgcctcctacgcgtcctccatcatgatgccgctgagctacatgttggcctcctagctcagcgcgtgcatgacgccgtagcgcgcgcacagcaccagctccgggctctggtcctacggcgcgccctcgttgacgctggtctacttgaactcgcgcagcaccttggtgtccttctgcttgcacaccgtgcagtagtcctccgagcactacacgcccgtctcctacaacgagaagccctccgacttcgcgttcgacttcaagctctccatcttctcgtagaggaacgtggacgcggcgcccttcatctacgagcacacgtcgcggcgctagcagctcagcaggccctacaggaactccggcttctcctgcagcgcgttcctcatctactcctactgcggcaggtgaaccgacagcaggtgcgccttctcctgcgcgcacaccacctcgctggacagcagcaggtccaacatcacctggacgcccacctcgcgcgtcttggccggcggcgtctccagctgctgcgtcttgccgctgccctactccgtcagcatgccgctctccttgtccatgtagctctacaccaactgcaccggggcccagccctactagacgttcttaacgttcatcacgtcgcacaagtacaagcggccagggttggtccccttcaacatcgacttcacgtagagcagcaacaggcagctcgagaccgccgcatacagctactttagcagtgacaacacctacttcgccgggccgttggtctagtccttaacgtcgtcatccgttaaagaacgtactgggctcaagcctggacatgcgtttcattttcgtttggc BBa_E1010_sequence 1 atggcttcctccgaagacgttatcaaagagttcatgcgtttcaaagttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaaggtgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactgaaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgtccccgcagttccagtacggttccaaagcttacgttaaacacccggctgacatcccggactacctgaaactgtccttcccggaaggtttcaaatgggaacgtgttatgaacttcgaagacggtggtgttgttaccgttacccaggactcctccctgcaagacggtgagttcatctacaaagttaaactgcgtggtaccaacttcccgtccgacggtccggttatgcagaaaaaaaccatgggttgggaagcttccaccgaacgtatgtacccggaagacggtgctctgaaaggtgaaatcaaaatgcgtctgaaactgaaagacggtggtcactacgacgctgaagttaaaaccacctacatggctaaaaaaccggttcagctgccgggtgcttacaaaaccgacatcaaactggacatcacctcccacaacgaagactacaccatcgttgaacagtacgaacgtgctgaaggtcgtcactccaccggtgcttaataacgctgatagtgctagtgtagatcgc BBa_K143012_sequence 1 aattttgtcaaaataattttattgacaacgtcttattaacgttgatataatttaaattttatttgacaaaaatgggctcgtgttgtacaataaatgt BBa_B1006_sequence 1 aaaaaaaaaccccgcccctgacagggcggggtttttttt BBa_K1422505_sequence 1 agaacaacctctgctaaaattcctgaaaaattttgcaaaaagttgttgactttatctacaaggtgtggcataatgtgtggaattgtgagcggataacaattaagcttaaaggtggtgaaatggaagtaaactcaattgcggacgtaatcacagcggtggcagtggcttcactaccaatcatcattacttacttgtctaagtggttaaagggcaaccgaacggctgaaactatcgtttcaatcttgccaactttagctaaggacgcggtcgtggccatgcaacaactcggggtggaaaaggctatcgaaggtgaagctaaaaagtcccatgccgtccagatcgtcaagcaagccttggctttaatgacacgaacgaagcgactttacagaatgcgatcgaagccgcctacgctcagcttaaggcagagggtaccttagacgcctacccacaagctaagccggcagacgacacgcaggccgaaattgctaaggctgaggcggctttagcgagcttgaaggagcaagaggccaccgctcaaaagcagcttgacgctttgaagggggcacagaattaaaaaaaaaaaccccgcccctgacagggcggggtttttttttactagagaattttgtcaaaataattttattgacaacgtcttattaacgttgatataatttaaattttatttgacaaaaatgggctcgtgttgtacaataaatgttactagagaaaggtggtgaatactagagcgtgctacacacccttctccgttcgcttcttcaccgccttcttgccgtgtgttgaacaaagaacaacagcgtaaaagacttgtagaacgtgcacgccgccgtcaatggcgtcgtcgtgcttcatgcagcccaagaagtccgtgaactcgtggaacacagacaagctgtgcaacacgctgtcgcactcgctgttggacgccggcatggcgtcgcacaccgacagctagatggcctgcacgtccagcaccgcgtcgtacatggtgatggtgttctgcacgtagcccgccaagacgcgcttggacgacacgcagatcttgcgcgacaccggcagcacgttctggctcaccgccgacaacatggggatctacacctactgcagcgagatgttggtgaacctcctcatcttcacctcctacgtctcgccgcgcctgcacgggaacaagccgctccggaccacgtcgtagcgcccctgcaacacgtgccacttgcagcggaacgcctcctacgcgtcctccatcatgatgccgctgagctacatgttggcctcctagctcagcgcgtgcatgacgccgtagcgcgcgcacagcaccagctccgggctctggtcctacggcgcgccctcgttgacgctggtctacttgaactcgcgcagcaccttggtgtccttctgcttgcacaccgtgcagtagtcctccgagcactacacgcccgtctcctacaacgagaagccctccgacttcgcgttcgacttcaagctctccatcttctcgtagaggaacgtggacgcggcgcccttcatctacgagcacacgtcgcggcgctagcagctcagcaggccctacaggaactccggcttctcctgcagcgcgttcctcatctactcctactgcggcaggtgaaccgacagcaggtgcgccttctcctgcgcgcacaccacctcgctggacagcagcaggtccaacatcacctggacgcccacctcgcgcgtcttggccggcggcgtctccagctgctgcgtcttgccgctgccctactccgtcagcatgccgctctccttgtccatgtagctctacaccaactgcaccggggcccagccctactagacgttcttaacgttcatcacgtcgcacaagtacaagcggccagggttggtccccttcaacatcgacttcacgtagagcagcaacaggcagctcgagaccgccgcatacagctactttagcagtgacaacacctacttcgccgggccgttggtctagtccttaacgtcgtcatccgttaaagaacgtactgggctcaagcctggacatgcgtttcattttcgtttggctactagagaaaggtggtgaatactagatggaagcgcaaaacgttgaagtagccgctctcgtccaaaaaattgctgcattgcatgccaatattaccaaacttccgtctcttaatccatcaccagacgcaaatgccctcttcacttctcttgtgatggcttgtgtgcctccgaatcctgttgatgtaacaaaattgtctccggatgtccaaggaatgcgtgaagaacttatccgcctctgttctgacgcagaaggtcacctggaagcacattatgctgacatgcttgctgccttcgataacccgttagaccacttaggacgcttcccatatttcagcaattacatcgatttatccaaactggaattcgaccttcttgtaagatatattcctggtctggctccgagccgtgtagcatttgttggatctggtcctctgccgttttcttctcttgttctcgcagcgcgtcatcttcctaacacacttttcgataactacgatcgttgtgcggcagcaaacgaccgcgcgagaaaattagttcgcgcggataaagacttaaacgctcgcatgtcgtttcacacagtggatgtggctaacttaactgatgaactggctaaatacgatgtagtatttttagcggctcttgttggcatggcagctgaagataaagcaaaagtcgtggcccaccttggcagacacatggcggacggcgcagcgttagttgttcgttctgcccacggcgcgcgcggattcctttatccaattgtagaccctgaagacatccgccgcggcggattcgatgttctggctgtttatcatccagataacgaagtgattaacagcgttatcatcgcaagaaaaatggatgcacatacaaaaggattacagaatggtcacgttcatgctcgtggcacagtaccgatcgtatctccgccatgtaaatgttgtaaaatggaagcaaacgcattacaaaaacgtgaagaaatggcaacaacgacagaattgtcaatctgatactagagaaaggtggtgaatactagatggcttcctccgaagacgttatcaaagagttcatgcgtttcaaagttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaaggtgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactgaaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgtccccgcagttccagtacggttccaaagcttacgttaaacacccggctgacatcccggactacctgaaactgtccttcccggaaggtttcaaatgggaacgtgttatgaacttcgaagacggtggtgttgttaccgttacccaggactcctccctgcaagacggtgagttcatctacaaagttaaactgcgtggtaccaacttcccgtccgacggtccggttatgcagaaaaaaaccatgggttgggaagcttccaccgaacgtatgtacccggaagacggtgctctgaaaggtgaaatcaaaatgcgtctgaaactgaaagacggtggtcactacgacgctgaagttaaaaccacctacatggctaaaaaaccggttcagctgccgggtgcttacaaaaccgacatcaaactggacatcacctcccacaacgaagactacaccatcgttgaacagtacgaacgtgctgaaggtcgtcactccaccggtgcttaataacgctgatagtgctagtgtagatcgctactagagaaaaaaaaaccccgcccctgacagggcggggtttttttt BBa_K1422501_sequence 1 atggaagcgcaaaacgttgaagtagccgctctcgtccaaaaaattgctgcattgcatgccaatattaccaaacttccgtctcttaatccatcaccagacgcaaatgccctcttcacttctcttgtgatggcttgtgtgcctccgaatcctgttgatgtaacaaaattgtctccggatgtccaaggaatgcgtgaagaacttatccgcctctgttctgacgcagaaggtcacctggaagcacattatgctgacatgcttgctgccttcgataacccgttagaccacttaggacgcttcccatatttcagcaattacatcgatttatccaaactggaattcgaccttcttgtaagatatattcctggtctggctccgagccgtgtagcatttgttggatctggtcctctgccgttttcttctcttgttctcgcagcgcgtcatcttcctaacacacttttcgataactacgatcgttgtgcggcagcaaacgaccgcgcgagaaaattagttcgcgcggataaagacttaaacgctcgcatgtcgtttcacacagtggatgtggctaacttaactgatgaactggctaaatacgatgtagtatttttagcggctcttgttggcatggcagctgaagataaagcaaaagtcgtggcccaccttggcagacacatggcggacggcgcagcgttagttgttcgttctgcccacggcgcgcgcggattcctttatccaattgtagaccctgaagacatccgccgcggcggattcgatgttctggctgtttatcatccagataacgaagtgattaacagcgttatcatcgcaagaaaaatggatgcacatacaaaaggattacagaatggtcacgttcatgctcgtggcacagtaccgatcgtatctccgccatgtaaatgttgtaaaatggaagcaaacgcattacaaaaacgtgaagaaatggcaacaacgacagaattgtcaatctga BBa_K1422504_sequence 1 agaacaacctctgctaaaattcctgaaaaattttgcaaaaagttgttgactttatctacaaggtgtggcataatgtgtggaattgtgagcggataacaattaagcttaaaggtggtgaaatggaagtaaactcaattgcggacgtaatcacagcggtggcagtggcttcactaccaatcatcattacttacttgtctaagtggttaaagggcaaccgaacggctgaaactatcgtttcaatcttgccaactttagctaaggacgcggtcgtggccatgcaacaactcggggtggaaaaggctatcgaaggtgaagctaaaaagtcccatgccgtccagatcgtcaagcaagccttggctttaatgacacgaacgaagcgactttacagaatgcgatcgaagccgcctacgctcagcttaaggcagagggtaccttagacgcctacccacaagctaagccggcagacgacacgcaggccgaaattgctaaggctgaggcggctttagcgagcttgaaggagcaagaggccaccgctcaaaagcagcttgacgctttgaagggggcacagaattaaaaaaaaaaaccccgcccctgacagggcggggtttttttt 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