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->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
annotation1683
1
stem_loop
range1683
1
13
35
annotation7019
1
BBa_B0011
range7019
1
1
46
BBa_K2088002
1
BBa_K2088002
dT+mhbR+mhbPt+GFP
2016-10-01T11:00:00Z
2016-10-19T01:59:53Z
PbaC comes from Sphingobium wenxiniae JZ-1, and it exists on the Scaffold 12, instead of the vector of pbaA1A2B.Sphingobium wenxiniae JZ-1 utilizes a wide range of pyrethroids and their metabolic product, 3-phenoxybenzoate, as sources of
carbon and energy.
GenBank: KJ009325.1
reference:
A Novel Angular Dioxygenase Gene Cluster Encoding 3-Phenoxybenzoate 1=,2=-Dioxygenase in Sphingobium wenxiniae JZ-1,
Chenghong Wang, Qing Chen, Rui Wang, Chao Shi, Xin Yan, Jian He, Qing Hong, Shunpeng Li
Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China.
PbaC is a 44-kDa protein that consists of 408 amino acids and contains a consensus motif for a flavin adenine dinucleotide-binding (ADP-binding) site (GXGX2GX3A
X6G)。Existing in Sphingobium wenxiniae JZ-1, it???s a glutathione reductase (GR)-type reductase gene. Though pbaC is the important gene to degrade 3-PBA as the first step, the transcriptional level of pbaC was far less than that of other genes like pbaA1A2B since it is not located in the immediate vicinity of pbaA1A2B. However, with the optimization of our experiment, the efficience of degradation on 3-pba has been improved.
false
false
_2556_
29893
33723
9
false
we have used diffrerent promotors and RBS to test the degrading efficience of pbaC. And we design the sequence as the part submission requests.
false
Yuxin He
component2522270
1
BBa_K2088004
component2522261
1
BBa_B0014
component2522265
1
BBa_K2088011
annotation2522265
1
BBa_K2088011
range2522265
1
102
1019
annotation2522270
1
BBa_K2088004
range2522270
1
1028
2348
annotation2522261
1
BBa_B0014
range2522261
1
1
95
BBa_K2088011
1
BBa_K2088011
MhbR: a protein that combines the 3HBA to induce the promoter Mhbpt.
2016-10-07T11:00:00Z
2016-10-14T07:22:34Z
The gene of MhbR can be gotten from the bacteria M5a1 using PCR.The sequence of the gene comes from GenBank https://www.ncbi.nlm.nih.gov/nuccore/EU165545.1
MhbR is a protein that can combine the 3HBA to induce the promoter Mhbpt.MhbR can be used in the induction system and the system will be induced when both of the MhbR and the 3-HBA exist. It can also be used as a section of the detection device when we need to degrade the 3-HBA.
false
false
_2556_
33751
29893
9
false
None
false
Shi Kejian
annotation2487580
1
MhbR coding region
range2487580
1
1
918
annotation2487579
1
TGA stop codon
range2487579
1
916
918
annotation2487578
1
ATG start codon
range2487578
1
1
3
BBa_K2088004
1
BBa_K2088004
Mhbpt+GFP
2016-10-08T11:00:00Z
2016-10-19T12:37:39Z
PbaC comes from Sphingobium wenxiniae JZ-1, and it exists on the Scaffold 12, instead of the vector of pbaA1A2B.Sphingobium wenxiniae JZ-1 utilizes a wide range of pyrethroids and their metabolic product, 3-phenoxybenzoate, as sources of
carbon and energy.
It???s a codon-optimized gene of pbaC(BBa_K2088003), and it can be used with provided standard restriction site (EcoRI,XbaI,SpeI,PstI) without destructing the functional region of pbaC.
PbaC is the phenoxybenzoic acid dioxygenase reductase on Sphingobium wenxiniae's genomic DNA and it codes a 44-kDa protein that consists of 408 amino acids and contains a consensus motif for a flavin adenine dinucleotide-binding (ADP-binding) site (GXGX2GX3AX6G)。Existing in Sphingobium wenxiniae JZ-1, it???s a glutathione reductase (GR)-type reductase gene. Though pbaC is the important gene to degrade 3-PBA as the first step, the transcriptional level of pbaC was far less than that of other genes like pbaA1A2B since it is not located in the immediate vicinity of pbaA1A2B. However, with the optimization of our experiment, the efficience of degradation on 3-pba has been improved.
false
false
_2556_
29893
33723
9
false
We optimaized the codon region of pbaC for a more convient use if other teams want to use it.
false
Yuxin He
annotation2489293
1
native RBS
range2489293
1
436
455
annotation2521997
1
GFP
range2521997
1
456
1173
annotation2489292
1
Mhbpt
range2489292
1
1
435
annotation2521999
1
T1 terminator
range2521999
1
1193
1321
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
annotation7020
1
BBa_B0012
range7020
1
1
41
annotation1687
1
stop
range1687
1
34
34
annotation1690
1
polya
range1690
1
28
41
annotation1686
1
T7 TE
range1686
1
8
27
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
component939303
1
BBa_B0012
component939311
1
BBa_B0011
annotation939311
1
BBa_B0011
range939311
1
50
95
annotation939303
1
BBa_B0012
range939303
1
1
41
BBa_B0014_sequence
1
tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattt
BBa_K2088002_sequence
1
tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattttactagatggcggactggacgcagaaagtgaagctgcaccatttacagatgctggtggcgctgggggagcaaggcaatctcacgcaggtggcgaaaatgatgaacattactcagcccgcgctctccaaatggctcagccagtttgaagacgaagtcggcatggttttgttcgaacgccatagcaaaggcctgcgcccgaccgaaggcgggaagctgctgcttcagcacgcccagcggctgattaacgatatgtcgcgttcgcagtatgagatcgagcgttttaagcagggcggacaggtgggcagcctgatgattggctgttcgccggtggcgaccgactgcgtctcgcaggcgatcctcgaactgctcaaagagatgccgaccctgcacctgaatatcgaagagaaggtcatgacgccgctgcttaacgatctgctcgccggcgtggtggatgtggttgtcggacgcgtcggcggacgggcgctggagctgccgctgagctaccgggtgctctacaccgaaccggtctgctttgtcgcccgtcccgatcacccgctggcccaaaaatcgcggttaagctgggccgatctctccccctggcgctggatcgtctggcccaccggcacgccaattcgcctgagcatcgacaacgcgctggtggataacggcgtgatgctgccggaaaacaccattgagtccgcctcgatgaacgtcaccagcaacctactgcaaagcagcgatatggtctcaattctctccttgcgtctggcgcagcgctacgccgcccagcaccagctggcgattcttaatttgccgcgcattgaacaaaaaggtagcgttggggtgttctggcgaaaaagtgaaacgccctcgctggcgctgagccggtttctgcactgcctgtcgctgcaatctacgctctgatactagaggctcgatctcatactgcgaacgcgacatatcgttaatcagccgctgggcgtgctgaagcagcagcttcccgccttcggtcgggcgcaggcctttgctatggcgttcgaacaaaaccatgccgacttcgtcttcaaactggctgagccatttggagagcgcgggctgagtaatgttcatcattttcgccacctgcgtgagattgccttgctcccccagcgccaccagcatctgtaaatggtgcagcttcactttctgcgtccagtccgccattagcgataacctccaggttatgtctatgcccgaaataccattgtacatttcattgcctgagttacaaactcgcaacataaaagaaataaatacaacacctacccctacctgcactgaggcataacgatgactcaacgacttgaattacagaagctgctcaacgctactagaggaaagaggagaaatactagatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggccctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcacctttcggtgggcctttctgcgtttatat
BBa_K2088004_sequence
1
gctcgatctcatactgcgaacgcgacatatcgttaatcagccgctgggcgtgctgaagcagcagcttcccgccttcggtcgggcgcaggcctttgctatggcgttcgaacaaaaccatgccgacttcgtcttcaaactggctgagccatttggagagcgcgggctgagtaatgttcatcattttcgccacctgcgtgagattgccttgctcccccagcgccaccagcatctgtaaatggtgcagcttcactttctgcgtccagtccgccattagcgataacctccaggttatgtctatgcccgaaataccattgtacatttcattgcctgagttacaaactcgcaacataaaagaaataaatacaacacctacccctacctgcactgaggcataacgatgactcaacgacttgaattacagaagctgctcaacgctactagaggaaagaggagaaatactagatgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggccctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcacctttcggtgggcctttctgcgtttatat
BBa_B0011_sequence
1
agagaatataaaaagccagattattaatccggcttttttattattt
BBa_B0012_sequence
1
tcacactggctcaccttcgggtgggcctttctgcgtttata
BBa_K2088011_sequence
1
atggcggactggacgcagaaagtgaagctgcaccatttacagatgctggtggcgctgggggagcaaggcaatctcacgcaggtggcgaaaatgatgaacattactcagcccgcgctctccaaatggctcagccagtttgaagacgaagtcggcatggttttgttcgaacgccatagcaaaggcctgcgcccgaccgaaggcgggaagctgctgcttcagcacgcccagcggctgattaacgatatgtcgcgttcgcagtatgagatcgagcgttttaagcagggcggacaggtgggcagcctgatgattggctgttcgccggtggcgaccgactgcgtctcgcaggcgatcctcgaactgctcaaagagatgccgaccctgcacctgaatatcgaagagaaggtcatgacgccgctgcttaacgatctgctcgccggcgtggtggatgtggttgtcggacgcgtcggcggacgggcgctggagctgccgctgagctaccgggtgctctacaccgaaccggtctgctttgtcgcccgtcccgatcacccgctggcccaaaaatcgcggttaagctgggccgatctctccccctggcgctggatcgtctggcccaccggcacgccaattcgcctgagcatcgacaacgcgctggtggataacggcgtgatgctgccggaaaacaccattgagtccgcctcgatgaacgtcaccagcaacctactgcaaagcagcgatatggtctcaattctctccttgcgtctggcgcagcgctacgccgcccagcaccagctggcgattcttaatttgccgcgcattgaacaaaaaggtagcgttggggtgttctggcgaaaaagtgaaacgccctcgctggcgctgagccggtttctgcactgcctgtcgctgcaatctacgctctga
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