BBa_K381001 1 BBa_K381001 Nitrate reporter: PyeaR - GFP composite 2010-10-04T11:00:00Z 2015-05-08T01:12:17Z Combination of two existing biobricks from the parts registry Released HQ 2013 Nitrate and Nitrite sensitive promoter PyeaR with a GFP coding device and strong RBS to create a nitrate-sensitive system which signals through expression of GFP. Optimum use appears to be when sensing nitrate within a range of 0 - 20 mM false false _487_ 0 6940 9 In stock true None false Katharine Coyte component2082866 1 BBa_B0030 component2082870 1 BBa_B0010 component2082872 1 BBa_B0012 component2082869 1 BBa_E0040 component2082864 1 BBa_K216005 annotation2082869 1 BBa_E0040 range2082869 1 130 849 annotation2082866 1 BBa_B0030 range2082866 1 109 123 annotation2082864 1 BBa_K216005 range2082864 1 1 100 annotation2082872 1 BBa_B0012 range2082872 1 946 986 annotation2082870 1 BBa_B0010 range2082870 1 858 937 BBa_K672000 1 BBa_K672000 Nitrate sensing at low temperatures. 2011-09-16T11:00:00Z 2015-05-08T01:13:03Z Pyear + RBS + GFP + TT + TT + hyBb + ompA + AOX. It comes from the combination of two other existing Biobricks. For more information consult both other parts: http://partsregistry.org/Part:BBa_K381001 http://partsregistry.org/Part:BBa_K410000 It's a combination of the biobricks BBa_k381001 (Pyear + RBS + GFP + TT + TT) and BBa_k410000 (hyBb + ompA + AOX). We are expecting our part to be able to sense nitrate and nitrites even after experiencing a cold shock at 20?? C, making our BB employable in other places where the temperatures can be as low as 15?? C. If you are interested in sensing nitrate at low temperatures false false _855_ 0 10335 9 It's complicated true We wanted to make sure that both parts worked in our specific conditions, and for that we did tests in the lab and by the moment everything is going good enough. false UTP-Panama Team component2131107 1 BBa_K410000 component2131124 1 BBa_K381001 annotation2131124 1 BBa_K381001 range2131124 1 1526 2511 annotation2131107 1 BBa_K410000 range2131107 1 1 1517 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 annotation7018 1 BBa_B0010 range7018 1 1 80 annotation4184 1 stem_loop range4184 1 12 55 BBa_B0030 1 BBa_B0030 RBS.1 (strong) -- modified from R. Weiss 2003-01-31T12:00:00Z 2015-08-31T04:07:20Z Released HQ 2013 Strong RBS based on Ron Weiss thesis. Strength is considered relative to <bb_part>BBa_B0031</bb_part>, <bb_part>BBa_B0032</bb_part>, <bb_part>BBa_B0033</bb_part>. false true _44_46_ 0 24 7 In stock false Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix (&quot;orig&quot; in figure 4-14 of Ron Weiss thesis). <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 <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. annotation7025 1 BBa_B0030 range7025 1 1 15 annotation1701 1 RBS-1\Strong range1701 1 1 15 annotation1702 1 RBS range1702 1 8 12 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 annotation7020 1 BBa_B0012 range7020 1 1 41 annotation1686 1 T7 TE range1686 1 8 27 annotation1687 1 stop range1687 1 34 34 BBa_K216005 1 BBa_K216005 PyeaR promoter, responsive to nitrate, nitrite and nitric oxide 2009-09-24T11:00:00Z 2015-05-08T01:11:30Z BioBricked from E. coli K-12 genomic DNA by the Edinburgh 2009 iGEM team. PyeaR promoter. This is the promoter of the Escherichia coli yeaR/yoaG operon (see Lin, H.-Y., Bledsoe, P.J., and Stewart, V. 2007. Activation of yeaR-yoaG operon transcription by the nitrate-responsive regulator NarL is independent of oxygen-responsive regulator Fnr in ''Escherichia coli'' K-12. J. Bacteriol. 189, 7539-7548). Unlike other E. coli promoters responding to nitrate and nitrite, this promoter is not repressed under aerobic conditions. false false _317_ 0 837 163 It's complicated true No special considerations. false Edinburgh iGEM 2009 annotation2027074 1 promoter -35 region range2027074 1 66 71 annotation2027075 1 promoter -10 region range2027075 1 89 94 annotation2027073 1 NsrR-binding region range2027073 1 58 80 annotation2027072 1 NarL-binding region range2027072 1 50 65 BBa_K410000 1 BBa_K410000 Periplasmic Heat Generation 2010-10-26T11:00:00Z 2015-05-08T01:12:25Z The part consists of three sub-parts with varying origins. The cold-shock promoter, HybB, was amplified using PCR from the biobrick BBa_J43001 in the Spring 2010 Distribution. OmpA was amplified from a commercial vector pFLAGS-CTS (Sigma), a plasmid that contains the 81 bp signal peptide. Aox1a, the alternative oxidase from Sacred Lotus, was synthesized commercially by Mr. Gene, Co. The sequence was taken from Genbank (GenBank: AB491175.1) and is from the Sacred Lotus (Nelumbo Nucifera). What it is: This part consists of hybB-ompA-AOX1A. HybB is a cold shock promoter. OmpA is a periplasmic targeting sequence, and AOX1A is a gene responsible for thermogenesis in the sacred lotus, a plant. What it does: Induces AOX1A expression in response to a cold shock. Here, we describe a "cold shock" as incubating E. coli between 20-30C for 10-12 hours. The part should produce a thermogenic response raising the temperature of the E. coli's immediate environment (plate or liquid cultures) above ambient temperature. false false _522_ 0 7842 9 It's complicated true Design considerations revolved primarily around targeting the AOX to the periplasm in order to localize AOX near its proper substrates. false Christina Graves, Scott Holmes annotation2111710 1 NotI Site range2111710 1 394 401 annotation2111604 1 AoxA (Alternative Oxidase) range2111604 1 483 1517 annotation2111563 1 OmpA range2111563 1 414 476 annotation2111504 1 HybB Cold Shock Promoter range2111504 1 1 393 annotation2111580 1 Ribosome Binding Site range2111580 1 402 407 annotation2111736 1 XmaI Site range2111736 1 477 482 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_B0010_sequence 1 ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc BBa_K410000_sequence 1 cgccgctatggactggataaagagatggtaatggatttctttcgtgagaataattcctgttctacgttgcgcttttttatggccggttatcgcctcgaaaattgatcaaacatacgtattatcttgctttaattaattacactaatgcttcttcccttcgttttagcgccccgccgcagtatcatgatatcgataaccataataaatgtgtggtaaatggcgcatcgatcgcattattgattttgcgattgaggcaaaatatatgccaggtcttcgcaacggaataactataaatgactggagataacaccctcatccattctcacggcattaaccgtcgtgatttcatgaagctttgtgcagcattagccgccaccatggggttaagtagcagcggccgcaggagatatcatatgaaaaagacagctatcgcgattgcagtggcactggctggtttcgctaccgttgcgcaagctcccgggatgatgaacagcaaactggcagctctgctgctgaaacaactgggttctgctaccgttcgtaccgtgacaatgggtcctctgaatgggattaccactgagtcctcgtgctttctgcatgcatctggtccggtcgttccaggtcgccgtacttggattcgcttttcttgtctgggagtccgtaatggttctaccagtgccctgaataacaaagagaaagaggagaaaggcgtccgtacaagttctactgttggtggcgccaatcgccctgaggataaaatgatcgtgtcctattggggtatgcctccggcaaatctgactaaaaaagacggctccgagtggaaatggaactcattccgtccatgggaaacctataaagccgatctgtcgatcgatctgaaaaaacaccatagcccggtgacgtttatggataaactggcctattggaccgttaaagccctgcgctatccgactgatattctgttccaaaaccgttatggctgtcgtgccatgatgctggagactgtggcggcagtaccagggatggttggggggatgctgctgcacctgaaatctctgcgtcgcttcgaacattctggtgggtggatcaaaacactgctggaagaagccgaaaacgagcgtatgcacctgatgaccttcatggaagtgtctcagccaaaatggtatgaacgtgccctggttgtagcagttcagggtgtgttcttcaacacgtattttctgggttatctgatcagccctcgcttcgctcatcgtgtggttggatatctggaggaggaagcaattcactcctataccgagtttctgaaagaactggacaaaggcaacatccagaacgtcccagcaccagcaattgccgtggattattggcaactgccaccggattctacgctgcgtgatgtggtgatggtcgtccgtgctgatgaagcacatcatcgtgacgtgaaccactttgccagcgacattcacgaccaaggctatgagctgaaagagtctcctgctcctctgggatatcattaa BBa_K381001_sequence 1 ttcccatctataatcctccctgattcttcgctgatatggtgctaaaaagtaaccaataaatggtatttaaaatgcaaattatcaggcgtaccctgaaacgtactagagattaaagaggagaaatactagatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata BBa_B0030_sequence 1 attaaagaggagaaa BBa_K672000_sequence 1 cgccgctatggactggataaagagatggtaatggatttctttcgtgagaataattcctgttctacgttgcgcttttttatggccggttatcgcctcgaaaattgatcaaacatacgtattatcttgctttaattaattacactaatgcttcttcccttcgttttagcgccccgccgcagtatcatgatatcgataaccataataaatgtgtggtaaatggcgcatcgatcgcattattgattttgcgattgaggcaaaatatatgccaggtcttcgcaacggaataactataaatgactggagataacaccctcatccattctcacggcattaaccgtcgtgatttcatgaagctttgtgcagcattagccgccaccatggggttaagtagcagcggccgcaggagatatcatatgaaaaagacagctatcgcgattgcagtggcactggctggtttcgctaccgttgcgcaagctcccgggatgatgaacagcaaactggcagctctgctgctgaaacaactgggttctgctaccgttcgtaccgtgacaatgggtcctctgaatgggattaccactgagtcctcgtgctttctgcatgcatctggtccggtcgttccaggtcgccgtacttggattcgcttttcttgtctgggagtccgtaatggttctaccagtgccctgaataacaaagagaaagaggagaaaggcgtccgtacaagttctactgttggtggcgccaatcgccctgaggataaaatgatcgtgtcctattggggtatgcctccggcaaatctgactaaaaaagacggctccgagtggaaatggaactcattccgtccatgggaaacctataaagccgatctgtcgatcgatctgaaaaaacaccatagcccggtgacgtttatggataaactggcctattggaccgttaaagccctgcgctatccgactgatattctgttccaaaaccgttatggctgtcgtgccatgatgctggagactgtggcggcagtaccagggatggttggggggatgctgctgcacctgaaatctctgcgtcgcttcgaacattctggtgggtggatcaaaacactgctggaagaagccgaaaacgagcgtatgcacctgatgaccttcatggaagtgtctcagccaaaatggtatgaacgtgccctggttgtagcagttcagggtgtgttcttcaacacgtattttctgggttatctgatcagccctcgcttcgctcatcgtgtggttggatatctggaggaggaagcaattcactcctataccgagtttctgaaagaactggacaaaggcaacatccagaacgtcccagcaccagcaattgccgtggattattggcaactgccaccggattctacgctgcgtgatgtggtgatggtcgtccgtgctgatgaagcacatcatcgtgacgtgaaccactttgccagcgacattcacgaccaaggctatgagctgaaagagtctcctgctcctctgggatatcattaatactagagttcccatctataatcctccctgattcttcgctgatatggtgctaaaaagtaaccaataaatggtatttaaaatgcaaattatcaggcgtaccctgaaacgtactagagattaaagaggagaaatactagatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata BBa_K216005_sequence 1 ttcccatctataatcctccctgattcttcgctgatatggtgctaaaaagtaaccaataaatggtatttaaaatgcaaattatcaggcgtaccctgaaacg BBa_E0040_sequence 1 atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa BBa_B0012_sequence 1 tcacactggctcaccttcgggtgggcctttctgcgtttata igem2sbol 1 iGEM to SBOL conversion Conversion of the iGEM parts registry to SBOL2.1 Chris J. Myers James Alastair McLaughlin 2017-03-06T15:00:00.000Z