BBa_K2055012 1 BBa_K2055012 Tetrathionate Hydrolase 2016-09-27T11:00:00Z 2016-09-28T04:14:05Z It comes from the Acidithiobacillus Ferrooxidans genome. Tetrathionate Hydrolase, TetH codon-optimized for Acidithiobacillus Ferrooxidans. It codes for the enzyme that converts tetrathionate to thiosulfate and sulfur. false false _2523_ 30725 30725 9 false It is an extracellular matrix enzyme for A. Ferrooxidans. false Carlos Vasquez BBa_K2055020 1 BBa_K2055020 Overexpression of TetH with heat shock promoter and Inverter. 2016-09-27T11:00:00Z 2016-09-28T06:23:20Z Composite part If the characterization of HS promoter + Inverter + RFP works, we will use this construct for our project, to recover Copper, Nickel and Zinc with Acidithiobacillus Ferrooxidans. false false _2523_ 30725 30725 9 false Not tested yet. false Raul Garza & Carlos Vasquez component2485379 1 BBa_B0034 component2485380 1 BBa_K2055012 component2485364 1 BBa_K2055009 component2485369 1 BBa_B0012 component2485363 1 BBa_B0034 component2485361 1 BBa_K2055013 component2485373 1 BBa_R0011 component2485365 1 BBa_K2055010 component2485367 1 BBa_B0034 component2485368 1 BBa_K2055007 component2485387 1 BBa_B0014 annotation2485380 1 BBa_K2055012 range2485380 1 1873 3375 annotation2485365 1 BBa_K2055010 range2485365 1 604 622 annotation2485373 1 BBa_R0011 range2485373 1 1792 1845 annotation2485369 1 BBa_B0012 range2485369 1 1743 1783 annotation2485379 1 BBa_B0034 range2485379 1 1855 1866 annotation2485361 1 BBa_K2055013 range2485361 1 1 89 annotation2485364 1 BBa_K2055009 range2485364 1 116 595 annotation2485368 1 BBa_K2055007 range2485368 1 649 1734 annotation2485367 1 BBa_B0034 range2485367 1 631 642 annotation2485363 1 BBa_B0034 range2485363 1 98 109 annotation2485387 1 BBa_B0014 range2485387 1 3384 3478 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_B0012 1 BBa_B0012 TE from coliphageT7 2003-01-31T12:00:00Z 2015-08-31T04:07:20Z Derived from the TE terminator of T7 bacteriophage between Genes 1.3 and 1.4 <genbank>V01146</genbank>. Released HQ 2013 Transcription terminator for the <i>E.coli</i> RNA polymerase. false false _1_ 0 24 7 In stock false <P> <P>Suggested by Sri Kosuri and Drew Endy as a high efficiency terminator. The 5' end cutoff was placed immediately after the TAA stop codon and the 3' end cutoff was placed just prior to the RBS of Gene 1.4 (before AAGGAG).<P> Use anywhere transcription should be stopped when the gene of interest is upstream of this terminator. false Reshma Shetty annotation1690 1 polya range1690 1 28 41 annotation1686 1 T7 TE range1686 1 8 27 annotation7020 1 BBa_B0012 range7020 1 1 41 annotation1687 1 stop range1687 1 34 34 BBa_R0011 1 lacI+pL Promoter (lacI regulated, lambda pL hybrid) 2003-01-31T12:00:00Z 2015-05-08T01:14:14Z represillator of Elowitz and Leibler (2000) Released HQ 2013 Inverting regulatory region controlled by LacI (<bb_part>BBa_C0010</bb_part>, <bb_part>BBa_C0011</bb_part>, etc.) <p> The PLlac 0-1 promoter is a hybrid regulatory region consisting of the promoter P(L) of phage lambda with the cI binding sites replaced with lacO1. The hybrid design allows for strong promotion that can nevertheless be tightly repressed by LacI, the Lac inhibitor (i.e. repressor) (<bb_part>BBa_C0010</bb_part>) ([LUTZ97]). The activity of the promoter can be regulated over a >600-fold range by IPTG in E.Coli DH5-alpha-Z1 (same paper reference). false true _1_ 0 24 7 In stock false <P> <P>hybrid promoter design to create strong promoter that is, at the same time, highly repressible. note that the upstream operator installed in this hybrid is slightly different than the one in the original source (Lutz and Bujard, 1997). the most upstream operator region is slightly truncated in the represillator version, so that both operators in the hybrid are the same sequence. see references for details. also, the sequence has been truncated after the transcriptional start site.<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 increase transcription. This part is incompatible with environments containing lactose or lactose analogs. true Neelaksh Varshney, Grace Kenney, Daniel Shen, Samantha Sutton annotation1999 1 lac O1 range1999 1 3 19 annotation2000 1 -35 range2000 1 20 25 annotation2002 1 -10 range2002 1 43 48 annotation2001 1 lac O1 range2001 1 26 42 annotation7064 1 BBa_R0011 range7064 1 1 54 BBa_B0014 1 BBa_B0014 double terminator (B0012-B0011) 2003-07-15T11:00:00Z 2015-08-31T04:07:20Z Released HQ 2013 Double terminator consisting of BBa_B0012 and BBa_B0011 false true _1_ 0 24 7 In stock false true Reshma Shetty component939311 1 BBa_B0011 component939303 1 BBa_B0012 annotation939311 1 BBa_B0011 range939311 1 50 95 annotation939303 1 BBa_B0012 range939303 1 1 41 BBa_K2055007 1 BBa_K2055007 LacI for Acidithiobacillus 2016-09-27T11:00:00Z 2016-09-28T06:11:09Z The RBS used is the BBa_B0034, the terminator is the BBA_B0012, the LacI reculated Promoter is the BBa_R0011. The sequence for the FUR Box was obtained from the results of the paper of Quatrini et al. (Citation in our wiki), choosing the Fur box with the best score. The sequence for the FUR protein was obtained from the Acidithiobacillus ferrooxidans genome. Inverter with Ferric Uptake Regulator & LacI. Activates gene expression in presence of iron. LacI and FUR proteins are optimized for Acidithiobacillus ferrooxidans. false false _2523_ 30725 30725 9 false It does not have a promoter. false Carmen Padilla, Melissa Gonzalez & Melissa Rios BBa_K2055010 1 BBa_K2055010 FUR Box 2016-09-27T11:00:00Z 2016-09-28T04:07:16Z It is the FUR Box with the highest score in the work of: Quatrini, R., Lefimil, C., Veloso, F. A., Pedroso, I., Holmes, D. S., & Jedlicki, E. (2007). Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans. Nucleic Acids Research, 35(7), 2153???2166. http://doi.org/10.1093/nar/gkm068 This is a FUR Box with high affinity to BBa_K2055009. In presence of iron, it will block the downstream transcription. false false _2523_ 30725 30725 9 false It needs iron to block transcription. false Carlos Vasquez BBa_K2055013 1 BBa_K2055013 Heat Shock Promoter 2016-09-27T11:00:00Z 2016-09-28T04:19:49Z Ribeiro, D. A., Del Bem, L. E., Vicentini, R., Ferraz, L. F., Murakami, M. T., & Ottoboni, L. M. (2011). The small heat shock proteins from Acidithiobacillus ferrooxidans: gene expression, phylogenetic analysis, and structural modeling. BMC microbiology, 11(1), 1. &#963;32-dependent promoter for for the Afe_1437 gene in Acidithiobacillus ferrooxidans false false _2523_ 30725 30725 9 false Putative promoter in Acidithiobacillus ferrooxidans. Must check its characterization. false Raul Garza BBa_K2055009 1 BBa_K2055009 FUR Protein 2016-09-27T11:00:00Z 2016-09-28T04:06:55Z The sequence for the FUR Box was obtained from the results of the paper of Quatrini et al. (Citation in our wiki). Ferric Uptace Regulator Protein codon-optimized for Acidithiobacillus Ferrooxidans, the FUR Protein in presence of iron will block the transcription because it will bind to its FUR Box. false false _2523_ 30725 30725 9 false You will have to add a FUR Box to repress the transcription with this FUR protein in presence of iron. false Carlos Vasquez BBa_B0011 1 BBa_B0011 LuxICDABEG (+/-) 2003-01-31T12:00:00Z 2015-08-31T04:07:20Z Derived from luxICDABEG operon terminator of Vibrio fischeri <genbank>AF170104</genbank>. Released HQ 2013 Bidirectional transcriptional terminator consisting of a 22 bp stem-loop.</p> false false _1_ 0 24 7 In stock false <P> <P>In the naturally-occuring sequence there is a mismatch in the stem of the stem loop. This can be corrected via an A-&gt;G mutation (at position 40 -- sequence coordinate/not MFOLD coordinate). The above sequence does not reflect this mutation (but the MFOLD image does). This terminator's location cannot be found using some inverted repeat detectors like PALINDROME because it is too short and contains a mismatch. This one was found with the help of Tom Knight. It lies between two coding regions that point towards eachother.<P> true Reshma Shetty annotation7019 1 BBa_B0011 range7019 1 1 46 annotation1683 1 stem_loop range1683 1 13 35 BBa_K2055007_sequence 1 atgaaacccgtaacgctctacgatgtggcggaatacgctggcgtgtcttaccagaccgtcagcagggttgtgaatcaagcctcccatgtatcggcgaaaacccgtgagaaagtggaggcggcaatggctgaactgaactatatcccaaaccgagttgctcaacagctcgcaggcaaacagagtctcctcattggcgtcgccacgtcctcgttggctctgcatgccccgagccagattgtggcggcgatcaagtcccgcgccgaccagcttggagcgtcggtggttgtctctatggtggaacggtcaggcgttgaggcgtgcaaggctgcggtacataacctgctggcccagcgagtaagcggcctcattattaactaccctctggacgatcaggacgctatcgctgtcgaggccgcatgtacaaacgtccccgccctgttcctcgacgtctcggatcagacgcccatcaacagtataattttttctcatgaagacggcacccggttaggcgttgagcatctggtagccttgggccaccagcagattgccctcctggcaggccctctttcgagtgtaagcgcccgcttgcgccttgcaggctggcataagtatcttacccgaaaccagatccagccgatcgcggaacgcgagggagattggtccgccatgtcaggatttcaacagacgatgcaaatgctcaacgaaggtatcgtaccgacggccatgttggtcgcgaacgaccaaatggccctgggcgcgatgcgggcgataacggaaagcggcctacgcgtcggagccgacatctcagtggtcggctacgacgatacggaagactcctcctgctatattccccccctcacgaccattaagcaggactttcgcctgttgggacaaacgtccgttgatcgactccttcagctgtcgcagggtcaagccgtgaaaggaaatcagctcctgcctgtcagtctggtgaaacgcaagaccaccttggcccccaatacccaaaccgccagcccccgcgcgcttgcggattctctcatgcagttggctagacaggttagtcgcctggaatcgggacagtgataa BBa_B0014_sequence 1 tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattt BBa_B0034_sequence 1 aaagaggagaaa BBa_K2055010_sequence 1 tgtaataagactcattcgt BBa_K2055020_sequence 1 actcgtacccataacgttgcatgccagagtccaggcgtacagtcgcttggctggcgtcctattgatgcccgtgaaggaggtgtaaaatgtactagagaaagaggagaaatactagatgattgatgagaggatgaactcggacgaactgaaacgggctggtctcaaggccaccctcccacgactcaagatcctacggatattcgaagattcggatgctcgacatctgaccgcaggtgagatctatcggctcttgctggaaaccggcgaagaagtgggcttggcgaccgtatatcgtgtactgacgcagttcgagatggcaggtttggtccgccgccatcattttgagggcgataaggccgtgttcgagctgaacgagaccggtcaccacgaccacatggtgtgtactgcgtgtggaaaggtgctcgagtttttcgacgaaatgctggaagcccggcaacgcgagctcgccgccaatcgcggtttcttcatttcggatcatagtctctatctttatggcacctgtctgggcatgcaggacgtgggaatctgctcgcttcgcgacgacgacgcgccaggtgccagtactgactgataatactagagtgtaataagactcattcgttactagagaaagaggagaaatactagatgaaacccgtaacgctctacgatgtggcggaatacgctggcgtgtcttaccagaccgtcagcagggttgtgaatcaagcctcccatgtatcggcgaaaacccgtgagaaagtggaggcggcaatggctgaactgaactatatcccaaaccgagttgctcaacagctcgcaggcaaacagagtctcctcattggcgtcgccacgtcctcgttggctctgcatgccccgagccagattgtggcggcgatcaagtcccgcgccgaccagcttggagcgtcggtggttgtctctatggtggaacggtcaggcgttgaggcgtgcaaggctgcggtacataacctgctggcccagcgagtaagcggcctcattattaactaccctctggacgatcaggacgctatcgctgtcgaggccgcatgtacaaacgtccccgccctgttcctcgacgtctcggatcagacgcccatcaacagtataattttttctcatgaagacggcacccggttaggcgttgagcatctggtagccttgggccaccagcagattgccctcctggcaggccctctttcgagtgtaagcgcccgcttgcgccttgcaggctggcataagtatcttacccgaaaccagatccagccgatcgcggaacgcgagggagattggtccgccatgtcaggatttcaacagacgatgcaaatgctcaacgaaggtatcgtaccgacggccatgttggtcgcgaacgaccaaatggccctgggcgcgatgcgggcgataacggaaagcggcctacgcgtcggagccgacatctcagtggtcggctacgacgatacggaagactcctcctgctatattccccccctcacgaccattaagcaggactttcgcctgttgggacaaacgtccgttgatcgactccttcagctgtcgcagggtcaagccgtgaaaggaaatcagctcctgcctgtcagtctggtgaaacgcaagaccaccttggcccccaatacccaaaccgccagcccccgcgcgcttgcggattctctcatgcagttggctagacaggttagtcgcctggaatcgggacagtgataatactagagtcacactggctcaccttcgggtgggcctttctgcgtttatatactagagaattgtgagcggataacaattgacattgtgagcggataacaagatactgagcacatactagagaaagaggagaaatactagatgccttcgattgtccggaaccacggaccccacaacaaaattctgctgagcgccctcctgctggcactgtttgggtgggtgcccctggcgagtgcggcggtcgccgtgcccatggattctacgggtccgtaccgcacggtttcccatcctgagaacgccccgtcgggcgtggatgctggcgtagggccaagtgaatggacccatgcgtatgccaacccggctcacaacgcagctttccccgtcccggacgacgcgcccgagtggattcgcaacggggtcagttggctgtttccggaggcgcgggcgtggcccctggctaaccctcctttcggatcgaaaacctatggtgctgcggaagccagcgtgacccagacgcagttctatggaaacgccctcggtccaagtgtcgtggatggagtggtctatgctgaatccgacgatatgtttgcgtatgcagtcaacgccaagacggggaagctgatctggcgcgcctcacccgtgggcaacaatttgatggggaacccgctcgtgattgggaacaccgtatacctgagtgccgggagcgtggcctttaactttgctaacgtcctgaggtatgcgcataacccctcggcaagcgcccgcggattaaacgtgtccttcaatggcatttatgcgctgaatcggtcgaatggcaaactcttgtggtattttgcgacgccgggtgagaccatggcgacgccggcttacgacaataacaccttgtttattgcggatggcgcaggcaacgcattcggcatcaatgcgacaacaggaaaacaggtctggaagacgcacgtgggcggcatggacaatatgagttccgtaaccgcttaccgacacaacatttacttcgccatggctattaagccgtatttgtattgcttgaacgagtccaacggccacatcgtctggaagggcacgatccctggcgccagcaatacgggcatcggagacgtcagccccgcggctgcggatggcgtggttgtactcgatgcgactaccaagccgcaagccaataaaaaagctatgttcagcaacgtgatccgtgcatttgacgccaaaaccggtgcagtgctctggacccgcaatatgggttcgggcggcaaaatccccgcctttaaaggtggcgtgcccatgatccacaataacattgtatatgtgggtaatccggtggcgagcacctaccaggcgtacgagctgaaaacgggaaagctgctgtggacctggcacgtccccaccaaggtagccgcaggtgcaggccgttcggccccgacatactacaagggcctgctttacatcacgaccggccagtatatctttgttgtcaatccggccaccggaaaagagctccatcagcatcatatcggtggtcaattcggtatcgaaagccctgtgatcgttggcggaacggtgtacctcaccaactcatgggattggataatggcaatccccctgaaaaccatttcgcacggctcgtgataatactagagtcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattt BBa_K2055013_sequence 1 actcgtacccataacgttgcatgccagagtccaggcgtacagtcgcttggctggcgtcctattgatgcccgtgaaggaggtgtaaaatg BBa_K2055012_sequence 1 atgccttcgattgtccggaaccacggaccccacaacaaaattctgctgagcgccctcctgctggcactgtttgggtgggtgcccctggcgagtgcggcggtcgccgtgcccatggattctacgggtccgtaccgcacggtttcccatcctgagaacgccccgtcgggcgtggatgctggcgtagggccaagtgaatggacccatgcgtatgccaacccggctcacaacgcagctttccccgtcccggacgacgcgcccgagtggattcgcaacggggtcagttggctgtttccggaggcgcgggcgtggcccctggctaaccctcctttcggatcgaaaacctatggtgctgcggaagccagcgtgacccagacgcagttctatggaaacgccctcggtccaagtgtcgtggatggagtggtctatgctgaatccgacgatatgtttgcgtatgcagtcaacgccaagacggggaagctgatctggcgcgcctcacccgtgggcaacaatttgatggggaacccgctcgtgattgggaacaccgtatacctgagtgccgggagcgtggcctttaactttgctaacgtcctgaggtatgcgcataacccctcggcaagcgcccgcggattaaacgtgtccttcaatggcatttatgcgctgaatcggtcgaatggcaaactcttgtggtattttgcgacgccgggtgagaccatggcgacgccggcttacgacaataacaccttgtttattgcggatggcgcaggcaacgcattcggcatcaatgcgacaacaggaaaacaggtctggaagacgcacgtgggcggcatggacaatatgagttccgtaaccgcttaccgacacaacatttacttcgccatggctattaagccgtatttgtattgcttgaacgagtccaacggccacatcgtctggaagggcacgatccctggcgccagcaatacgggcatcggagacgtcagccccgcggctgcggatggcgtggttgtactcgatgcgactaccaagccgcaagccaataaaaaagctatgttcagcaacgtgatccgtgcatttgacgccaaaaccggtgcagtgctctggacccgcaatatgggttcgggcggcaaaatccccgcctttaaaggtggcgtgcccatgatccacaataacattgtatatgtgggtaatccggtggcgagcacctaccaggcgtacgagctgaaaacgggaaagctgctgtggacctggcacgtccccaccaaggtagccgcaggtgcaggccgttcggccccgacatactacaagggcctgctttacatcacgaccggccagtatatctttgttgtcaatccggccaccggaaaagagctccatcagcatcatatcggtggtcaattcggtatcgaaagccctgtgatcgttggcggaacggtgtacctcaccaactcatgggattggataatggcaatccccctgaaaaccatttcgcacggctcgtgataa BBa_B0011_sequence 1 agagaatataaaaagccagattattaatccggcttttttattattt BBa_K2055009_sequence 1 atgattgatgagaggatgaactcggacgaactgaaacgggctggtctcaaggccaccctcccacgactcaagatcctacggatattcgaagattcggatgctcgacatctgaccgcaggtgagatctatcggctcttgctggaaaccggcgaagaagtgggcttggcgaccgtatatcgtgtactgacgcagttcgagatggcaggtttggtccgccgccatcattttgagggcgataaggccgtgttcgagctgaacgagaccggtcaccacgaccacatggtgtgtactgcgtgtggaaaggtgctcgagtttttcgacgaaatgctggaagcccggcaacgcgagctcgccgccaatcgcggtttcttcatttcggatcatagtctctatctttatggcacctgtctgggcatgcaggacgtgggaatctgctcgcttcgcgacgacgacgcgccaggtgccagtactgactgataa BBa_B0012_sequence 1 tcacactggctcaccttcgggtgggcctttctgcgtttata BBa_R0011_sequence 1 aattgtgagcggataacaattgacattgtgagcggataacaagatactgagcaca 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