BBa_K648011
1
BBa_K648011
Standard 25-Ready Xyle Reporter
2011-07-03T11:00:00Z
2015-05-08T01:12:59Z
The original genetic material for this part came from part BBa_K316007 which was mutated via PCR based site-directed mutagensis. The xyle portion of this large part was then amplified via PCR reaction and cloned into a new vector along with a prefix/suffix for standard 25 assembly.
This is a mutated version of the Xyle reporter gene which encodes for the enzyme catechol-2,3-dioxygenase (metapyrocatechase), which converts catechol to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde. This version of Xyle has been made compatible with standard 25 assembly methods by removing three restriction sites (two NgoMIV sites: at bp 315 and 486, as well as one AgeI site: at bp 837). These mutations were made synonymous with the original sequence and codon optimized for E. Coli.
Because of the synonymous mutations, this gene can be easily used to create fusion protein parts. For more information on the Xyle gene and its uses as a reporter see part BBa_J33204.
false
false
_825_
0
9871
9
In stock
true
The mutations in this gene were made so that they were synonymous and codon optimized for E. coli cells. The part also contains the prefix/suffix for standard 25 assembly with addition restriction sites NgoMIV and AgeI.
false
Jim Rose
annotation2122825
1
misc
range2122825
1
1
918
BBa_K648013
1
BBa_K648013
GFP with Standard 25 Prefix/Suffix
2011-07-03T11:00:00Z
2016-01-25T02:32:21Z
This part is similar to the part BBa_E0040 commonly used as a reporter.
This is the standard GFP protein reporter (E0040) cloned with the prefix/suffix required for standard 25 assembly. It can easily be used to create fusion proteins through this method.
false
false
_825_
4206
9871
9
In stock
false
This part contains the AgeI and NgoMIV sites as part of it's prefix/suffix that allows it to be used in standard 25 assembly.
It was synthesized through PCR oligo synthesis methods using the following primers:
Forward (56.88 degrees)
TATTGAATTCGCGGCCGCTTCTAGATGGCCGGCCGTAAAGGAGAAGAACTTTTC
Reverse (56.95 degrees)
AATACTGCAGCGGCCGCTACTAGTATTAACCGGTCTTGTCGTCATCATCTTTATAAT
false
Jim Rose
annotation2122827
1
misc
range2122827
1
1
735
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
annotation1687
1
stop
range1687
1
34
34
annotation1686
1
T7 TE
range1686
1
8
27
BBa_B0015
1
BBa_B0015
double terminator (B0010-B0012)
2003-07-16T11:00:00Z
2015-08-31T04:07:20Z
Released HQ 2013
Double terminator consisting of BBa_B0010 and BBa_B0012
false
true
_1_
0
24
7
In stock
false
true
Reshma Shetty
component1916612
1
BBa_B0012
component1916610
1
BBa_B0010
annotation1916610
1
BBa_B0010
range1916610
1
1
80
annotation1916612
1
BBa_B0012
range1916612
1
89
129
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_K648008
1
BBa_K648008
TEV protease cleaveage site with Standard 25 Prefix/Suffix
2011-07-03T11:00:00Z
2015-05-08T01:12:59Z
Phan, J., Zdanov, A., Evdokimov, A. G., Tropea, J. E., Peters, H. P. K., Kapust, R. B., Li,
M., Wlodawer, A., and Waugh, D. S. (2002). Structural basis for the substrate specificity
of tobacco etch virus protease. J. Biol. Chem. 277: 50564-50572.
This is the cleaveage site for th Tobacco etch virus(TEV) protease commonly used for cleaving fusion proteins. It encodes for the amino acids E N L Y F Q G which are cleaved by the TEV protease. This part also contains the prefix/suffix required for standard 25 assembly into fusion parts.
false
false
_825_
0
9871
9
In stock
false
This part contains the AgeI and NgoMIV sites as part of it's prefix/suffix that allows it to be used in standard 25 assembly.
This part was synthesized through PCR oligo synthesis methods using the following primers:
Forward
5'---ATTAGAATTCGCGGCCGCTTCTAGATGGCCGGCGAGAATTTGTATTTTCAGGG---3'
Reverse
5'---TAATCTGCAGCGGCCGCTACTAGTATTAACCGGTACCCTGAAAATACAAATTCTC---3'
false
Jim Rose
BBa_J23100
1
BBa_J23100
constitutive promoter family member
2006-08-03T11:00:00Z
2015-08-31T04:08:40Z
Isolated from library of promoters
Released HQ 2013
Replace later
false
true
_52_
0
483
95
In stock
true
N/A
true
John Anderson
BBa_K648014
1
BBa_K648014
Fast-Fusion GFP-Xyle Reporter (TEV cleaveage with small linker)
2011-07-04T11:00:00Z
2015-05-08T01:12:59Z
The design of this part was inspired by the Imperial College London 2010 iGEM Team's Fast-Response module, part BBa_K316007.
This is a fast-acting reporter using the Xyle gene (BBa_K648011) fused to GFP. In its normal un-cleaved state the polymerization ability necessary for enzymatic action is inactivated. Once the fusion protein is cleaved by the TEV protease the catechol-2,3-dioxygenase enzyme encoded by the Xyle gene is able to convert catechol to the bright yellow product 2-hydroxy-cis,cis-muconic semialdehyde. This reporter is able to produce a visible color response in a matter of minutes.
This version uses the TEV cleavage site (BBa_K648008) followed by the smallest of the three flexible fusion protein linkers (BBa_K648005). The linker is attached to the N-terminus of the Xyle gene.
false
false
_825_
0
9871
9
Not in stock
false
All parts were assembled via standard 25 assembly methods.
false
Jim Rose
component2122887
1
BBa_J23100
component2122892
1
BBa_K648008
component2122902
1
BBa_B0015
component2122889
1
BBa_B0034
component2122895
1
BBa_K648011
component2122893
1
BBa_K648005
component2122891
1
BBa_K648013
annotation2122889
1
BBa_B0034
range2122889
1
44
55
annotation2122891
1
BBa_K648013
range2122891
1
64
798
annotation2122887
1
BBa_J23100
range2122887
1
1
35
annotation2122895
1
BBa_K648011
range2122895
1
856
1773
annotation2122902
1
BBa_B0015
range2122902
1
1782
1910
annotation2122892
1
BBa_K648008
range2122892
1
807
827
annotation2122893
1
BBa_K648005
range2122893
1
836
847
BBa_K648005
1
BBa_K648005
Short Fusion Protein Linker: GGSG with standard 25 prefix/suffix
2011-07-02T11:00:00Z
2015-05-08T01:12:59Z
Patrick Argos, An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion, Journal of Molecular Biology, Volume 211, Issue 4, 20 February 1990, Pages 943-958, ISSN 0022-2836, DOI: 10.1016/0022-2836(90)90085-Z.
(http://www.sciencedirect.com/science/article/pii/002228369090085Z)
Ryoichi Arai,Hiroshi Ueda,Atsushi Kitayama,Noriho Kamiya,and Teruyuki Nagamune. Design of the linkers which effectively separate domains of a bifunctional fusion protein Protein Eng. (2001) 14(8): 529-532 doi:10.1093/protein/14.8.529
This is the shortest of the three fusion protein linkers created by the Penn State 2011 iGEM team. It encodes for the four amino acids GGSG and has a prefix and suffix compatible with assembly standard 25. It is used in one of the variants of our Fast-Fusion protein reporter system.
false
false
_825_
0
9871
9
In stock
false
This part contains the AgeI and NgoMIV sites as part of it's prefix/suffix that allows it to be used in standard 25 assembly.
This part was synthesized through PCR oligo synthesis methods using the following primers:
Forward (57.78 degrees)
TATTGAATTCGCGGCCGCTTCTAGATGGCCGGCggtggttctggtACC
Reverse (57.78 degrees)
AATACTGCAGCGGCCGCTACTAGTATTAACCGGTaccagaaccaccG
false
Jim Rose, Alex Bina, Ben Alouidor, Brian Avison
BBa_B0034
1
BBa_B0034
RBS (Elowitz 1999) -- defines RBS efficiency
2003-01-31T12:00:00Z
2015-08-31T04:07:20Z
Released HQ 2013
RBS based on Elowitz repressilator.
false
true
_1_
0
24
7
In stock
false
Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix. <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 for this part: <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.
annotation23325
1
conserved
range23325
1
5
8
BBa_K648014_sequence
1
ttgacggctagctcagtcctaggtacagtgctagctactagagaaagaggagaaatactagagcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaagattataaagatgatgacgacaagtactagaggagaatttgtattttcagggttactagagggtggttctggttactagagaacaaaggtgtaatgcgaccgggccatgtgcagctgcgtgtactggacatgagcaaggccctggaacactacgtcgagttgctgggcctgatcgagatggaccgtgacgaccagggccgtgtctatctgaaggcttggaccgaagtggataagttttccctggtgctacgcgaggctgacgagccgggcatggattttatgggtttcaaggttgtggatgaggatgctctccggcaactggagcgggatctgatggcatatggctgtgccgttgagcagctacccgcaggtgaactgaacagttgtggccgccgcgtgcgcttccaggccccctccgggcatcacttcgagttgtatgcagacaaggaatatactggaaagtggggtttgaatgacgtcaatcccgaggcatggccgcgcgatctgaaaggtatggcggctgtgcgtttcgaccacgccctcatgtatggcgacgaattgccagcgacctatgacctgttcaccaaggtgctcggtttctatctggccgaacaggtgctggacgaaaatggcacgcgcgtcgcccagtttctcagtctgtcgaccaaggcccacgacgtggccttcattcaccatccggaaaaaggccgcctccatcatgtgtccttccacctcgaaacctgggaagacttgcttcgcgccgccgacctgatctccatgaccgacacatctatcgatatcggcccaacccgccacggcctcactcacggcaagaccatctacttcttcgacccgtccggtaaccgcaacgaagtgttctgcgggggagattacaactacccggaccacaaaccagtgacctggaccaccgaccagctgggcaaggcgatcttttaccacgaccgcattctcaacgaacgattcatgaccgtgctgacctactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata
BBa_J23100_sequence
1
ttgacggctagctcagtcctaggtacagtgctagc
BBa_B0010_sequence
1
ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc
BBa_K648005_sequence
1
ggtggttctggt
BBa_B0034_sequence
1
aaagaggagaaa
BBa_K648011_sequence
1
aacaaaggtgtaatgcgaccgggccatgtgcagctgcgtgtactggacatgagcaaggccctggaacactacgtcgagttgctgggcctgatcgagatggaccgtgacgaccagggccgtgtctatctgaaggcttggaccgaagtggataagttttccctggtgctacgcgaggctgacgagccgggcatggattttatgggtttcaaggttgtggatgaggatgctctccggcaactggagcgggatctgatggcatatggctgtgccgttgagcagctacccgcaggtgaactgaacagttgtggccgccgcgtgcgcttccaggccccctccgggcatcacttcgagttgtatgcagacaaggaatatactggaaagtggggtttgaatgacgtcaatcccgaggcatggccgcgcgatctgaaaggtatggcggctgtgcgtttcgaccacgccctcatgtatggcgacgaattgccagcgacctatgacctgttcaccaaggtgctcggtttctatctggccgaacaggtgctggacgaaaatggcacgcgcgtcgcccagtttctcagtctgtcgaccaaggcccacgacgtggccttcattcaccatccggaaaaaggccgcctccatcatgtgtccttccacctcgaaacctgggaagacttgcttcgcgccgccgacctgatctccatgaccgacacatctatcgatatcggcccaacccgccacggcctcactcacggcaagaccatctacttcttcgacccgtccggtaaccgcaacgaagtgttctgcgggggagattacaactacccggaccacaaaccagtgacctggaccaccgaccagctgggcaaggcgatcttttaccacgaccgcattctcaacgaacgattcatgaccgtgctgacc
BBa_K648008_sequence
1
gagaatttgtattttcagggt
BBa_K648013_sequence
1
cgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaagattataaagatgatgacgacaag
BBa_B0012_sequence
1
tcacactggctcaccttcgggtgggcctttctgcgtttata
BBa_B0015_sequence
1
ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata
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