BBa_K836009 1 Lysis Lysis device for R. opacus 2012-09-19T11:00:00Z 2015-05-08T01:13:33Z The majority of the parts where made by backtranslating a protein. Others are existing biobricks while some are promoters obtained from databases as NCBI. Check each individual part to know its origin. Lysis construct based on the one presented by Berkeley's 2008 team BBa_K112022 (http://partsregistry.org/wiki/index.php?title=Part:BBa_K112022. It is based on the inducible expression of a lysozyme and lambda phage's holin in order to liberate internal products of the bacterial cell in an efficient way. The induction is achieved by the addition of nitrile or a similar agent since both genes are regulated by nitA promoter. false false _1095_ 0 11819 9 Not in stock false Constitutive expression of nitR and a low constitutive expression of an antiholin are required to avoid undesired lysis. false Ricardo Alvarado component2187640 1 BBa_B1006 component2187631 1 BBa_K143012 component2187616 1 BBa_B1006 component2187606 1 BBa_K836006 component2187628 1 BBa_B1006 component2187635 1 BBa_K836007 component2187602 1 BBa_K836005 component2187619 1 BBa_K143012 component2187611 1 BBa_B1006 component2187623 1 BBa_K836004 component2187598 1 BBa_K836008 annotation2187619 1 BBa_K143012 range2187619 1 1914 2010 annotation2187598 1 BBa_K836008 range2187598 1 1 115 annotation2187602 1 BBa_K836005 range2187602 1 124 1470 annotation2187640 1 BBa_B1006 range2187640 1 3506 3544 annotation2187628 1 BBa_B1006 range2187628 1 2365 2403 annotation2187606 1 BBa_K836006 range2187606 1 1479 1811 annotation2187623 1 BBa_K836004 range2187623 1 2019 2356 annotation2187611 1 BBa_B1006 range2187611 1 1820 1858 annotation2187631 1 BBa_K143012 range2187631 1 2412 2508 annotation2187616 1 BBa_B1006 range2187616 1 1867 1905 annotation2187635 1 BBa_K836007 range2187635 1 2517 3497 BBa_K836006 1 gpS Lysis protein S from Enterobacteria phage lambda (codon usage optimized for R. opacus) 2012-09-19T11:00:00Z 2015-05-08T01:13:32Z The amino sequence was obtained from Uniprot (http://www.uniprot.org/uniprot/P03705#section_seq lysis protein S) and optimized for R. opacus (avoiding standard restriction sites) using the free software GeneDesigner from DNA 2.0. This gene codifies for a protein that makes holes in the inner membrane of the bacterial cell. A Gram positive RBS (SpoVG, http://partsregistry.org/wiki/index.php?title=Part:BBa_K143021) was added at the beginning. false false _1095_ 0 11819 9 Not in stock false Between the RBS and the CDS a spacer consisting on a scar from a standard suffix and a preffix for CDS was inserted. false Ricardo Alvarado annotation2187525 1 SpoVG range2187525 1 1 12 annotation2187527 1 Spacer range2187527 1 13 18 annotation2187528 1 Holin range2187528 1 19 333 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_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_K836008 1 nitA promo nitA promoter 2012-09-19T11:00:00Z 2015-05-08T01:13:33Z Promoter taken from NCBI (http://www.ncbi.nlm.nih.gov/nucleotide/346420896?report=genbank&log$=nuclalign&blast_rank=1&RID=W0SH1PA7016). Promoter inducible by nitrile and similar agents. false false _1095_ 0 11819 9 Not in stock false The sequence was used as reported. false Ricardo Alvarado & Veronica Delgado annotation2187537 1 nitA promoter range2187537 1 1 115 BBa_K836007 1 nitR Nitrilase regulator from R. rhodochrous (codon usage optimized for R. opacus) 2012-09-19T11:00:00Z 2015-05-08T01:13:32Z The amino sequence was obtained from Uniprot (http://www.uniprot.org/uniprot/P72312) and then the condon usage was optimized for expression in R. opacus using the free software GeneDesigner from DNA 2.0. Protein in charge to regulate the expression of the genes put under control of nitA promoter. A Gram positive RBS (SpoVG http://partsregistry.org/wiki/index.php?title=Part:BBa_K143021) was inserted at the beginning. false false _1095_ 0 11819 9 Not in stock false A spacer which consist of the scar left by the assembly of a normal suffix and a CDS prefix was inserted between RBS and CDS. false Ricardo Alvarado & Veronica Delgado annotation2187535 1 Spacer range2187535 1 13 18 annotation2187534 1 SpoVG range2187534 1 1 12 annotation2187536 1 Nitrilase regulator range2187536 1 19 981 BBa_K836004 1 gpS Lysis inhibitor from Enterobacteria phage lambda (codon usage optimized for R. opacus) 2012-09-19T11:00:00Z 2015-05-08T01:13:32Z The amino sequence was obtained from Uniprot (http://www.uniprot.org/uniprot/P03705#section_seq lysis inhibitor isoform). The codon optimization for R. opacus (avoiding standard restriction sites EcoRI, PstI, XbaI and SpeI) was made using the free software GeneDesigner from DNA 2.0. This protein is the one in charge to avoid the formation of pores in the inner membrane of the bacterial cell. It has been optimized for expression in R. opacus. A weak RBS for Gram positive bacteria was used (http://partsregistry.org/Part:BBa_K090506:Design)in order to obtain low concentration of the protein. false false _1095_ 0 11819 9 Not in stock false We wanted a low concentration of this protein since medium to large concentrations could affect or completely inhibit the lysis device. Basal but constitutive expression of this protein is needed to avoid the formation of pores in the design lysis device. false Ricardo Alvarado annotation2187515 1 BBa_K090506 range2187515 1 1 11 annotation2187517 1 Lambda antiholin range2187517 1 18 338 annotation2187516 1 Scar range2187516 1 12 17 BBa_K836005 1 BBa_K836005 Lysozyme from Rhodococcus phage RER2 (codon usage optimized for R, opacus) 2012-09-19T11:00:00Z 2015-05-08T01:13:32Z The amino sequence was obtained from Uniprot (http://www.uniprot.org/uniprot/G9FHW6) and then it was optimized for R. opacus (avoiding standard restriction sites). Protein involved in the peptidoglycan degradation of the bacterial cell wall. A RBS for Gram positive bacteria (SpoVG) was added at the beginning. false false _1095_ 0 11819 9 Not in stock false A spacer was put between the RBS and the start codon which corresponds to the scar between a normal suffix and the prefix used for CDS to avoid RBS-CDS problems false Ricardo Alvarado annotation2187519 1 Scar range2187519 1 13 18 annotation2187518 1 SpoVG range2187518 1 1 12 annotation2187520 1 Lysozyme range2187520 1 19 1347 BBa_K836007_sequence 1 aaaggtggtgaatactagatgaacaccttcttctcctccgaccaggtctcggcgcccgaccgcgtcgcgctctggcacgacgtcatctgccgcagctacgtcccgctgaacatcaccctgaccagcgagcagcccttcatcggcaccgtctccaccggcaacctgggcaccgtccgcatcgccacgtcctcgtccctgccccagcagatcacccgcacccgccgcctgatccgccaggacgagcgcgagtacctcatggtcggcgtgcagtccgccggccacgccctcgtgcagcagcacggccgcaccgcccgcgtcggccgcggcggcctggtcttctgggacacccgccacccgtacgacatcctcttcccgaccgactggcgcatgagcgtcttccagttcccgcgctactccttcggcttcaccgaggacttcatcggccgcatgaccgccgtcaacgtcggcggcgaccgcggcatcggccgcgtggtctcctccttcatgaccagcatcaacgacgcgaccgacgccggcgacctggcggaggtcgcctccctccacaacagcgccgtcgacctgctgtccgcggcgatccggaccgagctggccgaccaggccgccgcctccgacggcctgctcgagtgcgtgctcgcctacatccgccagaacctggccgacccgaacctgtgcgcctcccagatcgccgccgagcacaacgtctccgtgcggaccctccaccgcctgttctcggccaccggccagggcgtggccgagcacatccgcaacctccgcctcgagcgcatcaagaccgagctggccgacccgaccagccggcgctacaccatcagcgccctggcgcgcaagtggggcttcctcgacccgtccaccttctcccgcgcgttcaaggacgcctacggcatcaccgcccgcgagtgggcggcctccgcctccgcctccccgaccgaggtctcgtaataa BBa_K836004_sequence 1 agaggtggtgttactagatgaaaatgcctgagaaacatgacctgctcgccgcaatcctggcagccaaggaacagggcattggcgccatcctggccttcgcgatggcgtatctccgcggtcggtacaacggcggagccttcaccaagaccgtcatcgacgcaaccatgtgcgcgatcatcgcatggttcatcagagatctcctggacttcgccggactgtcgtccaatctcgcctacatcacaagtgtgttcatcgggtacatcggcacggactccatcggctcgctgatcaagcggttcgccgccaagaaggcgggggttgaagacggtcgcaaccaa BBa_K836005_sequence 1 aaaggtggtgaatactagatggcacagcggctctggccactcccgcgcgacggctacgagctcacctccggtttcggaccccgctggggcgcacagcattccgggctagacctcgcggccccggacgggactccgttctacgcctgccaggcaggtaccgttcagttcatcggttccgcgacgggatacggccaatggctggtgatcgactcgtctgacgacgaggggtcgggttgtgtcgagtacggtcacatgtggaatgcccgagcgaccggcctctccgtgggagaccacgtagaggccggacagctcatcggctacattgggtcgaacggacagtcgaccggcccccacttgcacatcacggtttgggaacgtggctataactcggtccggatcgacccggaagtctggctggcaagcgcgggctttcccggggaggcggtcgcggccccgaagcccagtaccggcgagccgatctggggaatcgacgtgtctaaccaccaggggaacttcgacttcgcggcggcaaaggcggaggggttcgtgttcgcgacccataaggtgaccgaggcgaccgggtaccgagacccctactgggcgagggcccgccaggaaatggaaaagcatttccccggccggtggggaggatacgtgttctgccgaacgaatacggacccggtgaccgaagcgcgatatttctacgacgccgtgggaggtgacacctccgtgccggtccaaatcgattacgaagacaccaccaacggaggcagcggtgatgacctctgcaaccgcgtccgcgcgtatcaagacctgggcttccgcctgctacccatctatatcccgcgctggtactggcgagaccacatgggatcccccgatctctctggcctgcccgtaccgatctggaactcgcactacgcccggggcgtggactacgcctcaaatctgtacacgcagcatggcgagaaagccgaagcatggtccgacatgggcgggaagccggtcagtattctccagttttccgagaccgccatggtagcaggcaaactcatcgacgtgaacgccttccgcgggaccgaagccgagctcgatgagctcttctcggggcaagaactcagcatgagcgccgtgcaggagattaaggactacattgacgtgcgtgtcaccaacccgatcggctcggacgtcaaggacttgagggagcaggcctgcggccagggggcccgcgatgcaggccagtataacggctggccgcagttggggaaccgcacaattgccgacgccctcgcggtcatcggagttgctctgaagatagagggcttcttcgatccgaggagcataggc BBa_K143012_sequence 1 aattttgtcaaaataattttattgacaacgtcttattaacgttgatataatttaaattttatttgacaaaaatgggctcgtgttgtacaataaatgt BBa_B1006_sequence 1 aaaaaaaaaccccgcccctgacagggcggggtttttttt BBa_K836006_sequence 1 aaaggtggtgaatactagatgccagaaaagcacgacctactcgcagccatcctcgcggcaaaggagcagggcattggggcgatcctagctttcgcgatggcctacctccggggccgctacaacggcggtgcgttcaccaagacagtcatcgacgccactatgtgcgccatcattgcctggttcatccgagacctcctggacttcgctggactctcgtcgaacctggcgtacatcacctcagtcttcataggatacatcggcaccgactcaatcgggtctctcatcaagcggttcgcggccaagaaggccggtgtcgaggatgggcgcaaccaa BBa_K836009_sequence 1 gcgaactcccttatgcgggtggcgcagaatgccaggacccttgtcattccacgtcaattcatgcgccttttcacctcgtactgtcctgccaaacacaagcaacggaggtacggactactagagaaaggtggtgaatactagatggcacagcggctctggccactcccgcgcgacggctacgagctcacctccggtttcggaccccgctggggcgcacagcattccgggctagacctcgcggccccggacgggactccgttctacgcctgccaggcaggtaccgttcagttcatcggttccgcgacgggatacggccaatggctggtgatcgactcgtctgacgacgaggggtcgggttgtgtcgagtacggtcacatgtggaatgcccgagcgaccggcctctccgtgggagaccacgtagaggccggacagctcatcggctacattgggtcgaacggacagtcgaccggcccccacttgcacatcacggtttgggaacgtggctataactcggtccggatcgacccggaagtctggctggcaagcgcgggctttcccggggaggcggtcgcggccccgaagcccagtaccggcgagccgatctggggaatcgacgtgtctaaccaccaggggaacttcgacttcgcggcggcaaaggcggaggggttcgtgttcgcgacccataaggtgaccgaggcgaccgggtaccgagacccctactgggcgagggcccgccaggaaatggaaaagcatttccccggccggtggggaggatacgtgttctgccgaacgaatacggacccggtgaccgaagcgcgatatttctacgacgccgtgggaggtgacacctccgtgccggtccaaatcgattacgaagacaccaccaacggaggcagcggtgatgacctctgcaaccgcgtccgcgcgtatcaagacctgggcttccgcctgctacccatctatatcccgcgctggtactggcgagaccacatgggatcccccgatctctctggcctgcccgtaccgatctggaactcgcactacgcccggggcgtggactacgcctcaaatctgtacacgcagcatggcgagaaagccgaagcatggtccgacatgggcgggaagccggtcagtattctccagttttccgagaccgccatggtagcaggcaaactcatcgacgtgaacgccttccgcgggaccgaagccgagctcgatgagctcttctcggggcaagaactcagcatgagcgccgtgcaggagattaaggactacattgacgtgcgtgtcaccaacccgatcggctcggacgtcaaggacttgagggagcaggcctgcggccagggggcccgcgatgcaggccagtataacggctggccgcagttggggaaccgcacaattgccgacgccctcgcggtcatcggagttgctctgaagatagagggcttcttcgatccgaggagcataggctactagagaaaggtggtgaatactagatgccagaaaagcacgacctactcgcagccatcctcgcggcaaaggagcagggcattggggcgatcctagctttcgcgatggcctacctccggggccgctacaacggcggtgcgttcaccaagacagtcatcgacgccactatgtgcgccatcattgcctggttcatccgagacctcctggacttcgctggactctcgtcgaacctggcgtacatcacctcagtcttcataggatacatcggcaccgactcaatcgggtctctcatcaagcggttcgcggccaagaaggccggtgtcgaggatgggcgcaaccaatactagagaaaaaaaaaccccgcccctgacagggcggggtttttttttactagagaaaaaaaaaccccgcccctgacagggcggggtttttttttactagagaattttgtcaaaataattttattgacaacgtcttattaacgttgatataatttaaattttatttgacaaaaatgggctcgtgttgtacaataaatgttactagagagaggtggtgttactagatgaaaatgcctgagaaacatgacctgctcgccgcaatcctggcagccaaggaacagggcattggcgccatcctggccttcgcgatggcgtatctccgcggtcggtacaacggcggagccttcaccaagaccgtcatcgacgcaaccatgtgcgcgatcatcgcatggttcatcagagatctcctggacttcgccggactgtcgtccaatctcgcctacatcacaagtgtgttcatcgggtacatcggcacggactccatcggctcgctgatcaagcggttcgccgccaagaaggcgggggttgaagacggtcgcaaccaatactagagaaaaaaaaaccccgcccctgacagggcggggtttttttttactagagaattttgtcaaaataattttattgacaacgtcttattaacgttgatataatttaaattttatttgacaaaaatgggctcgtgttgtacaataaatgttactagagaaaggtggtgaatactagatgaacaccttcttctcctccgaccaggtctcggcgcccgaccgcgtcgcgctctggcacgacgtcatctgccgcagctacgtcccgctgaacatcaccctgaccagcgagcagcccttcatcggcaccgtctccaccggcaacctgggcaccgtccgcatcgccacgtcctcgtccctgccccagcagatcacccgcacccgccgcctgatccgccaggacgagcgcgagtacctcatggtcggcgtgcagtccgccggccacgccctcgtgcagcagcacggccgcaccgcccgcgtcggccgcggcggcctggtcttctgggacacccgccacccgtacgacatcctcttcccgaccgactggcgcatgagcgtcttccagttcccgcgctactccttcggcttcaccgaggacttcatcggccgcatgaccgccgtcaacgtcggcggcgaccgcggcatcggccgcgtggtctcctccttcatgaccagcatcaacgacgcgaccgacgccggcgacctggcggaggtcgcctccctccacaacagcgccgtcgacctgctgtccgcggcgatccggaccgagctggccgaccaggccgccgcctccgacggcctgctcgagtgcgtgctcgcctacatccgccagaacctggccgacccgaacctgtgcgcctcccagatcgccgccgagcacaacgtctccgtgcggaccctccaccgcctgttctcggccaccggccagggcgtggccgagcacatccgcaacctccgcctcgagcgcatcaagaccgagctggccgacccgaccagccggcgctacaccatcagcgccctggcgcgcaagtggggcttcctcgacccgtccaccttctcccgcgcgttcaaggacgcctacggcatcaccgcccgcgagtgggcggcctccgcctccgcctccccgaccgaggtctcgtaataatactagagaaaaaaaaaccccgcccctgacagggcggggtttttttt BBa_K836008_sequence 1 gcgaactcccttatgcgggtggcgcagaatgccaggacccttgtcattccacgtcaattcatgcgccttttcacctcgtactgtcctgccaaacacaagcaacggaggtacggac 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