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. annotation1701 1 RBS-1\Strong range1701 1 1 15 annotation1702 1 RBS range1702 1 8 12 annotation7025 1 BBa_B0030 range7025 1 1 15 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_K2056004 1 BBa_K2056004 NOx(Oxides of Nitrogen) sensor device (pNirK-Yellow chromoprotein) 2016-10-12T11:00:00Z 2016-10-13T01:10:17Z All parts in this sequence come from the Registry and have been listed. However, the complete part has been synthesized from IDT using their free gBLocks offer. This part is the oxides of nitrogen (NOx) sensing module of the 'Inspector NOxCO' device. 'Inspector NOxCO' is a bacterial sensor for carbon monoxide (CO) and oxides of nitrogen (NOx) in vehicle emissions. This part consists of the Anderson constitutive promoter(BBa_J23110) and RBS(B0030) with the coding sequence for NsrR(K2056001) a NOx sensitive repressor protein and single terminator(B0010) followed by NsrR repressed promoter pNirk(k2056002) with RBS(B0030) and 'Yellow chromoprotein'(K1033910) with terminator(BBa_B0012). If NOx are present, they will bind to the constitutive expressed NsrR that will relieve repression on the pNirK promoter activating transcription of the yellow chromoprotein. false false _2524_ 33019 33019 9 false The selection of the RBS and Constitutive promoter. Because of limitations of repeats that could be synthesized, we had to give up on the double terminators in the original design and go with single different terminators. A 70bp spacer(B0040) has been added for transcriptional efficiency. false Muhammad Ismail component2499271 1 BBa_B0040 component2499267 1 BBa_K2056001 component2499268 1 BBa_B0010 component2499263 1 BBa_J23110 component2499274 1 BBa_B0030 component2499265 1 BBa_B0030 component2499278 1 BBa_B0012 component2499272 1 BBa_K2056002 component2499277 1 BBa_K1033910 annotation2499263 1 BBa_J23110 range2499263 1 1 35 annotation2499265 1 BBa_B0030 range2499265 1 44 58 annotation2499278 1 BBa_B0012 range2499278 1 1730 1770 annotation2499272 1 BBa_K2056002 range2499272 1 667 978 annotation2499268 1 BBa_B0010 range2499268 1 501 580 annotation2499267 1 BBa_K2056001 range2499267 1 67 492 annotation2499274 1 BBa_B0030 range2499274 1 987 1001 annotation2499271 1 BBa_B0040 range2499271 1 589 658 annotation2499277 1 BBa_K1033910 range2499277 1 1008 1721 BBa_J23110 1 BBa_J23110 constitutive promoter family member 2006-08-16T11:00:00Z 2015-08-31T04:08:40Z Later Later false true _52_ 0 483 95 In stock true N/A true John Anderson BBa_K2056001 1 BBa_K2056001 NsrR - NO(x) sensitive pYear, pNirk repressor protein 2016-10-12T11:00:00Z 2016-10-13T10:04:47Z This part has been designed after the part Bba_K1682011 in the Registry of Standard Biological Parts. This part contains the NsrR (NO(x) sensitive pYear, pNirk repressor protein) encoding region. Escherichia coli (E. coli) detects environmental nitrate by the yeaR-yoaG operon. PyeaR is regulated by the NsrR repressor protein. Nitric oxide binds to the NsrR protein and relieves the repression on PyeaR. As a result, any genes that are downstream of PyeaR are expressed. This part is also related with BBa_K2056002, the promoter region of the NirK protein, because NsrR activates the transcription of NirK under high nitrite conditions. Due to these properties, we can use this part as a sensor for oxides of nitrogen. false false _2524_ 33019 33019 9 false Because the part Bba_K1682011 was not available from the registry, we had to get it synthesized. We had to codon optimized this part to conform to assembly standards and the requirements for synthesis. false Muhammad Ismail BBa_K2056002 1 BBa_K2056002 pNirK - promoter region 'nirK' (nitrite reductase) 2016-10-12T11:00:00Z 2016-10-13T10:23:32Z This part has been designed after the part BBa_K248002 in the Registry of Standard Biological Parts. This part is the promoter region of the nirK gene of Nitrosomonas europaea. The transcriptional regulatory factor NsrR (BBa_K2056001) controls transcription. false false _2524_ 33019 33019 9 false Because the part Bba_K1682011 was not available from the registry, we had to get it synthesized. We had to codon optimize this part to conform to assembly standards and the requirements for synthesis. false Muhammad Ismail BBa_K1033910 1 fwYellow fwYellow, yellow chromoprotein 2013-09-16T11:00:00Z 2016-01-25T02:41:53Z Synthetic chromoprotein from DNA 2.0. This chromoprotein naturally exhibits strong color when expressed. false false _1340_ 4206 13997 9 In stock false This construct is synthetic. It was synthesized from a template where the consensus sequence for the "color dependancy" in order to obtain a chromoprotein with a unique yellow color. false Sabri Jamal annotation2371218 1 fwYellow range2371218 1 1 711 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_B0040 1 spacer Spacer.1 (generic) 2003-01-31T12:00:00Z 2015-08-31T04:07:20Z Randomly generated and optimized for several parameters (see Design notes). Released HQ 2013 Generic spacer for ensuring a 70 bp distance between the end of the suffix of the BioBrick part containing the double terminator and the prefix of the BioBrick part containing the promoter of the new gene. Please, use the AlignX function of Vector NT to check for homology with the components in your plasmid before using this spacer.</P> false false _1_ 0 24 7 In stock false <P> <P><p>The size of the spacer was choosed to meet the minimum length of a sequence that can be queried using the BLAST search engine. However, subsequences of it can be used to design shorter spacers. The sequence was selected from many more sequences randomly generated using the <a href="http://www.lifesci.ucsb.edu/~maduro/random.htm">Random DNA Generator </a>engine; the GC% parameter used as input was 50%. The sequences were selected based on the following constraints listed in their order of importance: the absence of any putative promoter regions, a low degree of homology with the Elowitz plasmid (whose components are widely used in our designs), no homology with other <em>E.coli</em> sequences as shown by BLASTN search results and the presence of a number of TAA stop codons. The second constraint was the most stringent leading to the elimination of most sequences. </p> <p> DE made the following changes to the original sequence in order to add stop codons in the -3 frame and more in the +2 frame (note, not all of these stop codons are UAA. Thus, if used in an organism that inserts an amino acid @ UGA or UAG the obvious will occur):<br> T->A @ 85<br> T->A @ 42<br> C->T @ 79<br> A->T @ 64<br> A->T @ 31<br> T->A @ 34<br> C->A @ 37<br> Also, note that the above changes further reduce (the already very weak) homology to current NCBI-stored sequences.<br> </p> <P>In the process of selecting the best sequence it appeared that a good alternative sequence for a spacer would be: AGGTTCTGATATGTAACTGTGCCCAATGTCGTTAGTGACGCATACCTCTTAAGAGGCCACTGTCCTAACA. The sequence contains no putative promoters and shows moderate homology with the 5' end of the Ampicillin resistance gene. However a strong promoter sequence starts 12 bp downstream of this sequence, and therefore the sequence presented above was preferred. </p><P> The sequence is compatible (does not show significant homology) with the components in the Elowitz repressilator plasmid. true Vinay S. Mahajan, Brian Chow, Peter Carr annotation1721 1 Spacer-1 range1721 1 1 70 annotation7030 1 BBa_B0040 range7030 1 1 70 BBa_B0010_sequence 1 ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc BBa_B0040_sequence 1 aggttctgttaagtaactgaacccaatgtcgttagtgacgcttacctcttaagaggtcactgacctaaca BBa_K2056001_sequence 1 gtgcagttaacgagtttcactgattacggattacgtgcgctgatctacatggcgtcattgccagaagggcggatgaccagtatttctgaagtgactgacgtctacggcgtctcccgtaatcatatggtcaaaataatcaatcaacttagtcgtgccggctacgtgactgctgttcgtggaaaaaatggcggcattcgcctgggtaaaccggcgagtgcgatacgtattggtgatgtggtgcgcgagctggagcccttatcgctggtgaattgcagcagtgagttttgccacattacacctgcctgtaggttgaaacaggcactttctaaggccgtgcaaagttttcttacggaactggataactacacgcttgccgatttggttgaagagaatcaaccgctttataaattattgctggtggagtga BBa_K2056002_sequence 1 gttgcgcgtaatacggtcacgattcgtaatttccgtaacggaggacagtttctttcatttcagactgagatttccgaggatgcttaacgcgtgattgccgtgattcgccagtcccatgaagtccttccaatttattgagtgggcgttaataagtatattcctacattcttatttcttccagattggttaacgatctaaattgaacgcgtcaaaagcatcaaacgttatattaacaacattagtctgcgtggcggtgggtaatgatcgcctaagaagctgaacatgaccgtctttaagggcttatcctgtaga BBa_B0030_sequence 1 attaaagaggagaaa BBa_K1033910_sequence 1 atgacggcactgactgaaggcgcaaaactgttcgagaaagaaatcccatatatcactgagctggaaggtgacgttgaaggtatgaagtttatcatcaagggtgaaggtaccggtgacgcgagcgtcggtaaagtggatgctcagttcatttgtaccacgggcgacgttccggttccgtggagcacgctggtcaccacgctgacgtatggtgctcagtgctttgccaagtatccgcgccacattgcggatttcttcaaaagctgcatgccggaaggttacgtccaagagcgcaccatcacctttgagggtgatggcgtgttcaagacccgtgcggaagtcacctttgaaaatggcagcgtgtacaaccgtgtaaaactgaacggccagggtttcaagaaggacggccacgtgctgggcaaaaatctggagtttaactttacccctcattgtttgtacatttggggtgaccaagcgaatcatggcctgaagagcgcgttcaaaatcatgcatgagatcaccggctccaaagaggatttcattgttgccgatcacacccaaatgaataccccgattggtggtggtccggtgcacgtgccggagtaccaccacattacgtatcatgttaccctgtctaaagacgtcaccgatcaccgtgaccatttgaacattgttgaggtgatcaaggcagttgacctggagacgtaccgttaataa BBa_K2056004_sequence 1 tttacggctagctcagtcctaggtacaatgctagctactagagattaaagaggagaaatactagaggtgcagttaacgagtttcactgattacggattacgtgcgctgatctacatggcgtcattgccagaagggcggatgaccagtatttctgaagtgactgacgtctacggcgtctcccgtaatcatatggtcaaaataatcaatcaacttagtcgtgccggctacgtgactgctgttcgtggaaaaaatggcggcattcgcctgggtaaaccggcgagtgcgatacgtattggtgatgtggtgcgcgagctggagcccttatcgctggtgaattgcagcagtgagttttgccacattacacctgcctgtaggttgaaacaggcactttctaaggccgtgcaaagttttcttacggaactggataactacacgcttgccgatttggttgaagagaatcaaccgctttataaattattgctggtggagtgatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagaggttctgttaagtaactgaacccaatgtcgttagtgacgcttacctcttaagaggtcactgacctaacatactagaggttgcgcgtaatacggtcacgattcgtaatttccgtaacggaggacagtttctttcatttcagactgagatttccgaggatgcttaacgcgtgattgccgtgattcgccagtcccatgaagtccttccaatttattgagtgggcgttaataagtatattcctacattcttatttcttccagattggttaacgatctaaattgaacgcgtcaaaagcatcaaacgttatattaacaacattagtctgcgtggcggtgggtaatgatcgcctaagaagctgaacatgaccgtctttaagggcttatcctgtagatactagagattaaagaggagaaatactagatgacggcactgactgaaggcgcaaaactgttcgagaaagaaatcccatatatcactgagctggaaggtgacgttgaaggtatgaagtttatcatcaagggtgaaggtaccggtgacgcgagcgtcggtaaagtggatgctcagttcatttgtaccacgggcgacgttccggttccgtggagcacgctggtcaccacgctgacgtatggtgctcagtgctttgccaagtatccgcgccacattgcggatttcttcaaaagctgcatgccggaaggttacgtccaagagcgcaccatcacctttgagggtgatggcgtgttcaagacccgtgcggaagtcacctttgaaaatggcagcgtgtacaaccgtgtaaaactgaacggccagggtttcaagaaggacggccacgtgctgggcaaaaatctggagtttaactttacccctcattgtttgtacatttggggtgaccaagcgaatcatggcctgaagagcgcgttcaaaatcatgcatgagatcaccggctccaaagaggatttcattgttgccgatcacacccaaatgaataccccgattggtggtggtccggtgcacgtgccggagtaccaccacattacgtatcatgttaccctgtctaaagacgtcaccgatcaccgtgaccatttgaacattgttgaggtgatcaaggcagttgacctggagacgtaccgttaataatactagagtcacactggctcaccttcgggtgggcctttctgcgtttata BBa_J23110_sequence 1 tttacggctagctcagtcctaggtacaatgctagc BBa_B0012_sequence 1 tcacactggctcaccttcgggtgggcctttctgcgtttata 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