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 ("orig" 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