BBa_B0034 1 BBa_B0034 RBS (Elowitz 1999) -- defines RBS efficiency 2003-01-31T12:00:00Z 2015-08-31T04:07:20Z Released HQ 2013 RBS based on Elowitz repressilator. false true _1_ 0 24 7 In stock false Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix. <p>No secondary structures are formed in the given RBS region. Users should check for secondary structures induced in the RBS by upstream and downstream elements in the +50 to -50 region, as such structures will greatly affect the strength of the RBS. Contact info for this part: <a href="mailto:(bchow@media.mit.edu)">Brian Chow</a> true Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003. annotation23325 1 conserved range23325 1 5 8 BBa_M36252 1 BBa_M36252 Alkane Sensor Part 2011-12-09T12:00:00Z 2015-05-08T01:14:04Z original part Senses the presence of alkanes and produces a PoPS signal. false false _848_ 0 11079 9 Not in stock false We codon optimized this part for use in E. coli. false Evan Masutani, Erica Lieberman component2166623 1 BBa_B0010 component2166621 1 BBa_B0034 component2166619 1 BBa_J23106 component2166622 1 BBa_M36251 component2166625 1 BBa_M36250 annotation2166621 1 BBa_B0034 range2166621 1 44 55 annotation2166622 1 BBa_M36251 range2166622 1 62 2713 annotation2166619 1 BBa_J23106 range2166619 1 1 35 annotation2166625 1 BBa_M36250 range2166625 1 2808 2966 annotation2166623 1 BBa_B0010 range2166623 1 2722 2801 BBa_M36250 1 BBa_M36250 PalkB inducible promoter activated by AlkS 2011-12-09T12:00:00Z 2015-05-08T01:14:04Z Van Beilen, J.B., S. Panke, S. Lucchini, A.G. Franchini, M. Rothlisberger, and B. Witholt. "Analysis of Pseudomonas Putida Alkane Degradation Gene Clusters and &#64258;anking Insertion Sequences : Evolution and Regulation of the Alk Genes." Microbiology 147 (2001): 1621-630. This is a positively-regulated promoter derived from Pseudomonas putida and codon optimized for use in E. coli. In its native setting, PalkB is upstream of the AlkB gene in Pseudomonas putida and is actived by the presence of transcription factor AlkS. Transcription factor AlkS, also derived from P. putida, is known to bind to various alkanes and hydrocarbons, especially to medium-length alkanes. According to van Beilen, et al., 2001, the region that AlkS binds to is thought to be directly upstream of the -35 region of this promoter. Further analysis on m-fold reveals that this putative AlkS binding site readily forms a hairpin structure. This sequence is able to be synthesized from raw nucleotides, however, it appears that the sequence as given is flawed and acts constitutively rather than inducibly. This promoter acts strongly, regardless of whether alkane is present or not. It is currently hypothesized that other external factors act to govern this part's usability, as previous attempts to utilize this part in conjunction with AlkS in E. coli have succeeded. Specifically, the work of Panke, et al., 1999, obtained a working PalkB promoter by excising a 273-bp fragment from P. putida utilizing restriction enzymes. The sequence constructed in this work is 159-bp and, as stated before, derived from the work of van Beilen, et al., 2001, however, efforts were made to utilize only the promoter fragment while omitting the RBS and introductory sequence of the AlkB gene. false false _848_ 0 11079 9 Not in stock false When designing this part, efforts were made to extract only the promoter sequence while omitting the surrounding base-pairs as presented by van Beilen, et al., 2001. This may have proven to be a fatal flaw, as it is thought that the original surrounding sequences contribute to the functionality of the part as a whole. false Evan Masutani and Erica Lieberman BBa_M36251 1 BBa_M36251 AlkS Transcription Factor 2011-12-09T12:00:00Z 2015-05-08T01:14:04Z http://www.ncbi.nlm.nih.gov/protein/Q9L4M7.1 AlkS transcription factor is derived from Pseudomonas putida. It typically binds to medium chain length alkanes to change into its activated state. Once in its activated state, AlkS binds to its positively-regulated promoter, PalkB, and permits the sequence downstream of PalkB to be transcribed. false false _848_ 0 11079 9 Not in stock false We codon optimized this gene for use in E. coli. false Evan Masutani, Erica Lieberman BBa_J23106 1 BBa_J23106 constitutive promoter family member 2006-08-13T11:00:00Z 2015-08-31T04:08:40Z Isolated from library of promoters Released HQ 2013 Later false true _52_ 0 483 95 In stock true N/A true John Anderson BBa_B0010 1 BBa_B0010 T1 from E. coli rrnB 2003-11-19T12:00:00Z 2015-08-31T04:07:20Z Transcriptional terminator consisting of a 64 bp stem-loop. false false _1_ 0 24 7 In stock false true Randy Rettberg annotation4184 1 stem_loop range4184 1 12 55 annotation7018 1 BBa_B0010 range7018 1 1 80 BBa_B0010_sequence 1 ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc BBa_B0034_sequence 1 aaagaggagaaa BBa_M36251_sequence 1 atgaaaatcaaaatcattaacaacgatttcccggtagccaaaatcggcctggaccgtattacgactttggttagcgcgaaagtccacaactgcatctaccgcccgcgtctgtccatcgctgacggcacggctccacgtgtgtgcctgtaccgcgctccgccgggctacggcaaaaccgtggccttagcatttgaatggctgcgtcaccgtaccaccggccgtccggctgtttggatctcactgcgcgcgtctagttatagcgaattcgacatttgcgccgagatcatcgagcaactggaagcctttgagctggtaaccttctcccacgttcgcgaaggcgtgtcaaaaccgaccctcctacgtgatctggcgagttctctgtggcagtctacctcttctaacgaaatcgaaaccctgatctgcctcgataacatcaatcagggtctgggtctgccgctgttacatgctctgatggaattcatgctggaaactccgaaaagcatccgttttgcggtcgctggtaataccattaaaggctttagccgtctgaaactagcgggcgcgatgcaggaacacaccgaaaaggatttagccttcagtgcggacgaagcggtggccctggtggaggcggaagcggtgctgggtgtttccgaagtgcagatcgaggcgctggtgcaggaaatggaaggctggcctgttctgatcggtttcctcttgaaatgcgaactgccggcgaaaagtatctcaacagtggttgagatcgataactacttcaatgacgaaatcttcgaagctctgccggaacgttaccgcgttttcctggttaacagcagcctgctggatgttgtgacccctgacggctacaactacgtattcaagtgcgtcaatgcggcgtcatgtatcaaatacctgagcaccaattacatgctgttacgccacgtggaaggcgagccggcccagttcacactgcacccggtgctgcgtgactttctgcagggtattgcgtgggcggagaaccctgccaagcgcagctacctactgaaacgtgcggccttttggcactggcgtcgcggtgaataccagtacgctatccgtatcgctctgcgcgcgaacgattgccgttgggcagtgggtatgtctgaaggcattatcctggacttatcttttcgccagggtgaaatcgatacattacgtcattggctatctgagctgccggtgaaagacctgcacaaaaacccgatcgttcttatctgttttgcttgggtgctgtacttcagtcagcagtcagcccgcgccgagaaactgttaaaagacttgatcaccccgccggataagaaaaacaaatggcaggaaaaaggttggcctcaattagttttcgctatcggtaaagcgaccaacgacgaaatgctgctgtccgaagaactgtgcaacaaatggatcagtctgttcggcgattccaacgctgtaggtaaaggcgctgcgctgacctgccttgcgttcatcttcgcctccgaatatcgtttcgcagaactggaaaaagtcctcgctcaggcgcaggccgtgaacaagtttgccaaacaggacttcgcattcggttggctgtacgtcgctaagctgcagcaggccctcgccagcggtaaaatgtcttgggctcgtcagttgattactcaggcgcgcacagactccggtgcgcagattatggaaactgcgtttacctctaaaatgctcgacgcccttgaattagaaagtaattatgaactgtgccgtttagacacttccgaagagaaattctctgaaattctggagttcattgctaatcatggcgtcactgacgtgtttttttctgtttgtcgtgtggtatctgcctggcgccttggccgcaacgacctgaacggctccatcgaaatcctggagtgggctaaggcgtacgctgctgagaaaaacctcccgcgcctggaagtaatgagccaaattgagatctaccagcgtttacttttccagggagtcacctacatcaacaccctgcaggcatttgaggatcgtaaaattttttcaggtccccactccgcgccgctgaaagcgcgcctgctgcttgtacagagcctggcgctgagccgtgaccagaacttccatcttgcggcccaccgtgcgctgctggctatccagcaagcgcgtaaaattagcgcgggccagctggaagttcgtggtctgctgtacctcgcaggcgctcaggctggcggcggtactctgaaaaaagctcagcataatatcgcatacgccctggaaatggccaaacagctgcagtgcttccaaaccgtgctggacgaaatccgtcttatcaaacgtctgatcccgacgagctgcgaagttttcgcggcagtgaacctggaccaggcgatcggtgcgttttctcttccgcagatggtggaaatccgcaaatccgccgaaaacaaagcaggggacttcctgacgctgaaacaggtgtcggtactgaaactggtaaaagaaggttgctccaacaaacagattgcaaccaaaatgtatgtgaccgaagatgccatcaaatggcatatgcgcaaaatctttacgattcttaacgtcaaaagccgcacccaggctatcatcgaagctgaacgtcaaggcgtcatttaa BBa_J23106_sequence 1 tttacggctagctcagtcctaggtatagtgctagc BBa_M36252_sequence 1 tttacggctagctcagtcctaggtatagtgctagctactagagaaagaggagaaatactagatgaaaatcaaaatcattaacaacgatttcccggtagccaaaatcggcctggaccgtattacgactttggttagcgcgaaagtccacaactgcatctaccgcccgcgtctgtccatcgctgacggcacggctccacgtgtgtgcctgtaccgcgctccgccgggctacggcaaaaccgtggccttagcatttgaatggctgcgtcaccgtaccaccggccgtccggctgtttggatctcactgcgcgcgtctagttatagcgaattcgacatttgcgccgagatcatcgagcaactggaagcctttgagctggtaaccttctcccacgttcgcgaaggcgtgtcaaaaccgaccctcctacgtgatctggcgagttctctgtggcagtctacctcttctaacgaaatcgaaaccctgatctgcctcgataacatcaatcagggtctgggtctgccgctgttacatgctctgatggaattcatgctggaaactccgaaaagcatccgttttgcggtcgctggtaataccattaaaggctttagccgtctgaaactagcgggcgcgatgcaggaacacaccgaaaaggatttagccttcagtgcggacgaagcggtggccctggtggaggcggaagcggtgctgggtgtttccgaagtgcagatcgaggcgctggtgcaggaaatggaaggctggcctgttctgatcggtttcctcttgaaatgcgaactgccggcgaaaagtatctcaacagtggttgagatcgataactacttcaatgacgaaatcttcgaagctctgccggaacgttaccgcgttttcctggttaacagcagcctgctggatgttgtgacccctgacggctacaactacgtattcaagtgcgtcaatgcggcgtcatgtatcaaatacctgagcaccaattacatgctgttacgccacgtggaaggcgagccggcccagttcacactgcacccggtgctgcgtgactttctgcagggtattgcgtgggcggagaaccctgccaagcgcagctacctactgaaacgtgcggccttttggcactggcgtcgcggtgaataccagtacgctatccgtatcgctctgcgcgcgaacgattgccgttgggcagtgggtatgtctgaaggcattatcctggacttatcttttcgccagggtgaaatcgatacattacgtcattggctatctgagctgccggtgaaagacctgcacaaaaacccgatcgttcttatctgttttgcttgggtgctgtacttcagtcagcagtcagcccgcgccgagaaactgttaaaagacttgatcaccccgccggataagaaaaacaaatggcaggaaaaaggttggcctcaattagttttcgctatcggtaaagcgaccaacgacgaaatgctgctgtccgaagaactgtgcaacaaatggatcagtctgttcggcgattccaacgctgtaggtaaaggcgctgcgctgacctgccttgcgttcatcttcgcctccgaatatcgtttcgcagaactggaaaaagtcctcgctcaggcgcaggccgtgaacaagtttgccaaacaggacttcgcattcggttggctgtacgtcgctaagctgcagcaggccctcgccagcggtaaaatgtcttgggctcgtcagttgattactcaggcgcgcacagactccggtgcgcagattatggaaactgcgtttacctctaaaatgctcgacgcccttgaattagaaagtaattatgaactgtgccgtttagacacttccgaagagaaattctctgaaattctggagttcattgctaatcatggcgtcactgacgtgtttttttctgtttgtcgtgtggtatctgcctggcgccttggccgcaacgacctgaacggctccatcgaaatcctggagtgggctaaggcgtacgctgctgagaaaaacctcccgcgcctggaagtaatgagccaaattgagatctaccagcgtttacttttccagggagtcacctacatcaacaccctgcaggcatttgaggatcgtaaaattttttcaggtccccactccgcgccgctgaaagcgcgcctgctgcttgtacagagcctggcgctgagccgtgaccagaacttccatcttgcggcccaccgtgcgctgctggctatccagcaagcgcgtaaaattagcgcgggccagctggaagttcgtggtctgctgtacctcgcaggcgctcaggctggcggcggtactctgaaaaaagctcagcataatatcgcatacgccctggaaatggccaaacagctgcagtgcttccaaaccgtgctggacgaaatccgtcttatcaaacgtctgatcccgacgagctgcgaagttttcgcggcagtgaacctggaccaggcgatcggtgcgttttctcttccgcagatggtggaaatccgcaaatccgccgaaaacaaagcaggggacttcctgacgctgaaacaggtgtcggtactgaaactggtaaaagaaggttgctccaacaaacagattgcaaccaaaatgtatgtgaccgaagatgccatcaaatggcatatgcgcaaaatctttacgattcttaacgtcaaaagccgcacccaggctatcatcgaagctgaacgtcaaggcgtcatttaatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagatggctaatattattcagataactacaccaaggagtagttgaagcaggcttaaggtgagtgcagttttaccatgtcagatgtgagagtagatggcctgattttccctgttgggacaggaattaggttgtgtggtgctcgcagagacttattggacaata BBa_M36250_sequence 1 atggctaatattattcagataactacaccaaggagtagttgaagcaggcttaaggtgagtgcagttttaccatgtcagatgtgagagtagatggcctgattttccctgttgggacaggaattaggttgtgtggtgctcgcagagacttattggacaata 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