BBa_K352001 1 BBa_K352001 CooA from Rhodospirillum rubrum 2010-10-01T11:00:00Z 2015-05-08T01:12:11Z Hwan Youn, Robert L. Kerby, Mary Conrad, et al. 2004. Functionally Critical Elements of CooA-Related CO Sensors. J. Bacteriol. 186(5):1320-1329. doi:10.1128/JB.186.5.1320-1329.2004. CooA is a heme-containing transcriptional activator that enables Rhodospirillum rubrum to sense and grow on CO as a sole energy source. CooA is a member of a family of transcriptional regulators similar to the cAMP receptor protein and fumavate nitrate reduction from Escherichia coli. The protein is active in sequence-specific DNA binding in the presence of CO, but not in the absence of CO. The protein to be a dimer in the absence of CO. The product, CooA, is 28% identical (51% similar) to CRP(cAMP receptor protein) and 18% identical (45% similar) to FNR(fumavate nitrate reduction) from Escherichia coli. Inactive Fe(II) CooA structure adapted from that of the strain with PDB identification no. 1FT9. The protein consists of two monomers, shaded differently, which dimerize along the central C-helices of adjacent effector-binding domains. The solved structure is asymmetric, in which one monomer contains fused C- and D-helices. Nonetheless, both F-helices that interact with DNA in a sequence-specific manner are buried from the surface in the structure. The 4/5 loop is noted and so are the Pro2 and His77 heme Fe(II) ligands. false false _474_606_ 0 5815 9 It's complicated true The sequence information was acquired from NCBI and physical DNA was synthesized from GENEART. Classical cloning strategies(restriction digestion) were used to produce biobricks. false Cihan Tastan annotation2081251 1 Start Codon range2081251 1 1 3 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 annotation7030 1 BBa_B0040 range7030 1 1 70 annotation1721 1 Spacer-1 range1721 1 1 70 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_K2056003 1 BBa_K2056003 Carbon Monoxide sensor device (pCooF-Blue Chromoprotein) 2016-10-12T11:00:00Z 2016-10-13T12:36:12Z 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 carbon monoxide (CO) 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 CooA(BBa_K352001) a CO dependent transcriptional activator and single terminator(B0010) followed by CooA activated strong promoter pCooF(K352002) with RBS(B0030) and 'amilCP, blue chromoprotein' with terminator(BBa_B0012). If CO is present, the constitutive expressed CooA will bind to it and then bind to the pCOoF promoter activating transcription of the blue 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 component2499210 1 BBa_B0030 component2499200 1 BBa_B0040 component2499191 1 BBa_J23110 component2499197 1 BBa_B0010 component2499214 1 BBa_B0012 component2499213 1 BBa_K592009 component2499193 1 BBa_B0030 component2499208 1 BBa_K352002 component2499196 1 BBa_K352001 annotation2499197 1 BBa_B0010 range2499197 1 742 821 annotation2499213 1 BBa_K592009 range2499213 1 1031 1699 annotation2499200 1 BBa_B0040 range2499200 1 830 899 annotation2499191 1 BBa_J23110 range2499191 1 1 35 annotation2499210 1 BBa_B0030 range2499210 1 1010 1024 annotation2499196 1 BBa_K352001 range2499196 1 65 733 annotation2499193 1 BBa_B0030 range2499193 1 44 58 annotation2499208 1 BBa_K352002 range2499208 1 908 1001 annotation2499214 1 BBa_B0012 range2499214 1 1708 1748 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. annotation1702 1 RBS range1702 1 8 12 annotation1701 1 RBS-1\Strong range1701 1 1 15 annotation7025 1 BBa_B0030 range7025 1 1 15 BBa_K592009 1 amilCP amilCP, blue chromoprotein 2011-09-17T11:00:00Z 2015-05-08T01:12:48Z Acropora millepora Released HQ 2013 This chromoprotein, amilCP, naturally exhibits very strong color when expressed. The color is blue/purple and is visible to naked eye, thereby requiring no instruments to observe. This DNA was provided by Jeffrey Miller at UCLA. It was made BioBrick-compatible after removal of one illegal internal restriction site (EcoRI). false false _763_ 0 7929 9 In stock true Illegal internal restriction site had to be removed (EcoRI). false Lei Sun annotation2131628 1 amilCP range2131628 1 1 666 BBa_K352002 1 BBa_K352002 pCooF Promoter from Rhodospirillum rubrum 2010-10-01T11:00:00Z 2015-05-08T01:12:11Z S.W. Singer, M.B. Hirst and P.W. Ludden, CO-dependent H2 evolution by Rhodospirillum rubrum: role of CODH:CooF complex, Biochim Biophys Acta - Bioenerg 1757 (2006), pp. 1582???1591 CooA is a CO-sensing protein that activates the transcription of genes encoding the CO-oxidation (coo) regulon, whose polypeptide products are required for utilizing CO as an energy source in Rhodospirillum rubrum. CooA binds to a position overlapping the -35 element of the P(cooF) promoter, similar to the arrangement of class II CRP (cAMP receptor protein)- and FNR (fumarate and nitrate reductase activator protein)-dependent promoters when expressed in Escherichia coli. The CO-dependent anaerobic growth of Rhodospirillum rubrum relies on a CO oxidation system encoded by two CO regulated transcriptional units, cooMKLXUH and cooFSCTJ. The key products of the coo regulon are an O2- sensitive CO dehydrogenase (CooS), a CooS-associated Fe-S protein (CooF), and a CO-tolerant hydrogenase (CooH), and the expression of the genes depends upon the activity of the CooA protein, which senses CO under anaerobic conditions. CO-independent basal level transcription of PcooF is not detectable due to the absence of active CooA. false false _474_ 0 5815 9 It's complicated false The sequence information was acquired from NCBI and physical DNA was synthesized from GENEART. Classical cloning strategies(restriction digestion) were used to produce biobricks. false Ozkan IS annotation2081255 1 -10 Region range2081255 1 79 84 annotation2081253 1 CooA binding site range2081253 1 41 44 annotation2081254 1 CooA binding site range2081254 1 52 56 annotation2081252 1 A+T rich sequence range2081252 1 8 33 annotation2081257 1 Protected by CooA range2081257 1 36 61 annotation2081256 1 Transcription Start range2081256 1 92 93 annotation2081258 1 Protected by CooA+RNAP range2081258 1 23 91 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_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_B0010_sequence 1 ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc BBa_B0040_sequence 1 aggttctgttaagtaactgaacccaatgtcgttagtgacgcttacctcttaagaggtcactgacctaaca BBa_K352001_sequence 1 atgccaccacgcttcaatattgcaaacgtactgctgtctcctgatggtgagacgttcttccgcggttttcgctctaagattcatgcgaaaggctctctggtatgtactggtgaaggtgatgaaaacggtgtttttgttgtggttgatggtcgcctgcgtgtttacctggttggtgaggagcgtgagattagcctgttctacctgacttccggcgatatgttctgcatgcattccggctgcctggttgaagccaccgagcgcaccgaagtgcgtttcgccgatatccgcacgttcgagcagaaactgcaaacctgtccgtctatggcatggggcctgatcgccattctgggccgtgctctgacctcctgtatgcgtaccatcgaagacctgatgttccacgatattaaacaacgtatcgcgggctttttcatcgaccacgctaacactaccggtcgccagactcagggtggcgtaattgtttctgttgacttcactgtagaggaaatcgctaatctgatcggtagctcccgccagactactagcacggcgctgaactctctgattaaagagggttacatctcccgccagggccgtggtcactatactatcccgaacctggttcgcctgaaggcggctgcggatggtgaccgcgatgacgatgacgattga BBa_B0030_sequence 1 attaaagaggagaaa BBa_K592009_sequence 1 atgagtgtgatcgctaaacaaatgacctacaaggtttatatgtcaggcacggtcaatggacactactttgaggtcgaaggcgatggaaaaggtaagccctacgagggggagcagacggtaaagctcactgtcaccaagggcggacctctgccatttgcttgggatattttatcaccacagtgtcagtacggaagcataccattcaccaagtaccctgaagacatccctgactatgtaaagcagtcattcccggagggctatacatgggagaggatcatgaactttgaagatggtgcagtgtgtactgtcagcaatgattccagcatccaaggcaactgtttcatctaccatgtcaagttctctggtttgaactttcctcccaatggacctgtcatgcagaagaagacacagggctgggaacccaacactgagcgtctctttgcacgagatggaatgctgctaggaaacaactttatggctctgaagttagaaggaggcggtcactatttgtgtgaatttaaaactacttacaaggcaaagaagcctgtgaagatgccagggtatcactatgttgaccgcaaactggatgtaaccaatcacaacaaggattacacttcggttgagcagtgtgaaatttccattgcacgcaaacctgtggtcgcctaataa BBa_K352002_sequence 1 ttcggcgtcttttcatacccccataaaaactctggataactgtcatctggccgacagacggggccgggctttttgtcgcttactcggcgccagg BBa_K2056003_sequence 1 tttacggctagctcagtcctaggtacaatgctagctactagagattaaagaggagaaatactagatgccaccacgcttcaatattgcaaacgtactgctgtctcctgatggtgagacgttcttccgcggttttcgctctaagattcatgcgaaaggctctctggtatgtactggtgaaggtgatgaaaacggtgtttttgttgtggttgatggtcgcctgcgtgtttacctggttggtgaggagcgtgagattagcctgttctacctgacttccggcgatatgttctgcatgcattccggctgcctggttgaagccaccgagcgcaccgaagtgcgtttcgccgatatccgcacgttcgagcagaaactgcaaacctgtccgtctatggcatggggcctgatcgccattctgggccgtgctctgacctcctgtatgcgtaccatcgaagacctgatgttccacgatattaaacaacgtatcgcgggctttttcatcgaccacgctaacactaccggtcgccagactcagggtggcgtaattgtttctgttgacttcactgtagaggaaatcgctaatctgatcggtagctcccgccagactactagcacggcgctgaactctctgattaaagagggttacatctcccgccagggccgtggtcactatactatcccgaacctggttcgcctgaaggcggctgcggatggtgaccgcgatgacgatgacgattgatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagaggttctgttaagtaactgaacccaatgtcgttagtgacgcttacctcttaagaggtcactgacctaacatactagagttcggcgtcttttcatacccccataaaaactctggataactgtcatctggccgacagacggggccgggctttttgtcgcttactcggcgccaggtactagagattaaagaggagaaatactagatgagtgtgatcgctaaacaaatgacctacaaggtttatatgtcaggcacggtcaatggacactactttgaggtcgaaggcgatggaaaaggtaagccctacgagggggagcagacggtaaagctcactgtcaccaagggcggacctctgccatttgcttgggatattttatcaccacagtgtcagtacggaagcataccattcaccaagtaccctgaagacatccctgactatgtaaagcagtcattcccggagggctatacatgggagaggatcatgaactttgaagatggtgcagtgtgtactgtcagcaatgattccagcatccaaggcaactgtttcatctaccatgtcaagttctctggtttgaactttcctcccaatggacctgtcatgcagaagaagacacagggctgggaacccaacactgagcgtctctttgcacgagatggaatgctgctaggaaacaactttatggctctgaagttagaaggaggcggtcactatttgtgtgaatttaaaactacttacaaggcaaagaagcctgtgaagatgccagggtatcactatgttgaccgcaaactggatgtaaccaatcacaacaaggattacacttcggttgagcagtgtgaaatttccattgcacgcaaacctgtggtcgcctaataatactagagtcacactggctcaccttcgggtgggcctttctgcgtttata 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