BBa_K2056003
type: ComponentDefinition
persistent identity: BBa K2056003
display id: BBa_K2056003
version: 1
was generated by: iGEM to SBOL conversion
description: Carbon Monoxide sensor device (pCooF-Blue Chromoprotein)
created: 2016-10-12T11:00:00Z
modified: 2016-10-13T12:36:12Z
mutable provenance: 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.
owned by: james
owned by: myers
mutable description: 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.
discontinued: false
dominant: false
group u list: _2524_
m user id: 33019
owner id: 33019
owning group id: 9
status: status/Planning
bookmark: false
mutable notes: 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.
star: false
creator: Muhammad Ismail
type: DnaRegion
role: partType/Project
role: SO:0000804
component: BBa_B0040
component: BBa_B0010
component: BBa_B0030
component: BBa_K352002
component: BBa_B0012
component: BBa_K592009
component: BBa_J23110
component: BBa_K352001
sequence annotation: BBa_J23110
sequence annotation: BBa_B0030
sequence annotation: BBa_K352001
sequence annotation: BBa_B0010
sequence annotation: BBa_B0040
sequence annotation: BBa_K352002
sequence annotation: BBa_K592009
sequence annotation: BBa_B0012
sequence: https://synbiohub.org/public/igem/BBa_K2056003_sequence/1

BBa_B0040
type: Component
persistent identity: component2499200
display id: component2499200
version: 1
top level: BBa_K2056003
definition: spacer
access: public

BBa_B0010
type: Component
persistent identity: component2499197
display id: component2499197
version: 1
top level: BBa_K2056003
definition: BBa_B0010
access: public

BBa_B0030
type: Component
persistent identity: component2499210
display id: component2499210
version: 1
top level: BBa_K2056003
definition: BBa_B0030
access: public

BBa_K352002
type: Component
persistent identity: component2499208
display id: component2499208
version: 1
top level: BBa_K2056003
definition: BBa_K352002
access: public

BBa_B0012
type: Component
persistent identity: component2499214
display id: component2499214
version: 1
top level: BBa_K2056003
definition: BBa_B0012
access: public

BBa_K592009
type: Component
persistent identity: component2499213
display id: component2499213
version: 1
top level: BBa_K2056003
definition: amilCP
access: public

BBa_J23110
type: Component
persistent identity: component2499191
display id: component2499191
version: 1
top level: BBa_K2056003
definition: BBa_J23110
access: public

BBa_K352001
type: Component
persistent identity: component2499196
display id: component2499196
version: 1
top level: BBa_K2056003
definition: BBa_K352001
access: public

BBa_B0030
type: Component
persistent identity: component2499193
display id: component2499193
version: 1
top level: BBa_K2056003
definition: BBa_B0030
access: public

BBa_J23110
type: SequenceAnnotation
persistent identity: annotation2499191
display id: annotation2499191
version: 1
top level: BBa_K2056003
location: https://synbiohub.org/public/igem/BBa_K2056003/annotation2499191/range2499191/1
component: BBa_J23110

https://synbiohub.org/public/igem/BBa_K2056003/annotation2499191/range2499191/1
type: Range
persistent identity: range2499191
display id: range2499191
version: 1
top level: BBa_K2056003
direction: direction/reverse
start: 1
end: 35
orientation: inline

BBa_B0030
type: SequenceAnnotation
persistent identity: annotation2499193
display id: annotation2499193
version: 1
top level: BBa_K2056003
location: https://synbiohub.org/public/igem/BBa_K2056003/annotation2499193/range2499193/1
component: BBa_B0030

https://synbiohub.org/public/igem/BBa_K2056003/annotation2499193/range2499193/1
type: Range
persistent identity: range2499193
display id: range2499193
version: 1
top level: BBa_K2056003
direction: direction/forward
start: 44
end: 58
orientation: inline

BBa_K352001
type: SequenceAnnotation
persistent identity: annotation2499196
display id: annotation2499196
version: 1
top level: BBa_K2056003
location: https://synbiohub.org/public/igem/BBa_K2056003/annotation2499196/range2499196/1
component: BBa_K352001

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type: Range
persistent identity: range2499196
display id: range2499196
version: 1
top level: BBa_K2056003
direction: direction/reverse
start: 65
end: 733
orientation: inline

BBa_B0010
type: SequenceAnnotation
persistent identity: annotation2499197
display id: annotation2499197
version: 1
top level: BBa_K2056003
location: https://synbiohub.org/public/igem/BBa_K2056003/annotation2499197/range2499197/1
component: BBa_B0010

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type: Range
persistent identity: range2499197
display id: range2499197
version: 1
top level: BBa_K2056003
direction: direction/forward
start: 742
end: 821
orientation: inline

BBa_B0040
type: SequenceAnnotation
persistent identity: annotation2499200
display id: annotation2499200
version: 1
top level: BBa_K2056003
location: https://synbiohub.org/public/igem/BBa_K2056003/annotation2499200/range2499200/1
component: BBa_B0040

https://synbiohub.org/public/igem/BBa_K2056003/annotation2499200/range2499200/1
type: Range
persistent identity: range2499200
display id: range2499200
version: 1
top level: BBa_K2056003
direction: direction/forward
start: 830
end: 899
orientation: inline

BBa_K352002
type: SequenceAnnotation
persistent identity: annotation2499208
display id: annotation2499208
version: 1
top level: BBa_K2056003
location: https://synbiohub.org/public/igem/BBa_K2056003/annotation2499208/range2499208/1
component: BBa_K352002

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type: Range
persistent identity: range2499208
display id: range2499208
version: 1
top level: BBa_K2056003
direction: direction/reverse
start: 908
end: 1001
orientation: inline

BBa_B0030
type: SequenceAnnotation
persistent identity: annotation2499210
display id: annotation2499210
version: 1
top level: BBa_K2056003
location: https://synbiohub.org/public/igem/BBa_K2056003/annotation2499210/range2499210/1
component: BBa_B0030

https://synbiohub.org/public/igem/BBa_K2056003/annotation2499210/range2499210/1
type: Range
persistent identity: range2499210
display id: range2499210
version: 1
top level: BBa_K2056003
direction: direction/forward
start: 1010
end: 1024
orientation: inline

BBa_K592009
type: SequenceAnnotation
persistent identity: annotation2499213
display id: annotation2499213
version: 1
top level: BBa_K2056003
location: https://synbiohub.org/public/igem/BBa_K2056003/annotation2499213/range2499213/1
component: BBa_K592009

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type: Range
persistent identity: range2499213
display id: range2499213
version: 1
top level: BBa_K2056003
direction: direction/reverse
start: 1031
end: 1699
orientation: inline

BBa_B0012
type: SequenceAnnotation
persistent identity: annotation2499214
display id: annotation2499214
version: 1
top level: BBa_K2056003
location: https://synbiohub.org/public/igem/BBa_K2056003/annotation2499214/range2499214/1
component: BBa_B0012

https://synbiohub.org/public/igem/BBa_K2056003/annotation2499214/range2499214/1
type: Range
persistent identity: range2499214
display id: range2499214
version: 1
top level: BBa_K2056003
direction: direction/forward
start: 1708
end: 1748
orientation: inline

BBa_B0012
type: ComponentDefinition
persistent identity: BBa B0012
display id: BBa_B0012
version: 1
was generated by: iGEM to SBOL conversion
description: TE from coliphageT7
created: 2003-01-31T12:00:00Z
modified: 2015-08-31T04:07:20Z
mutable provenance: Derived from the TE terminator of T7 bacteriophage between Genes 1.3 and 1.4 <genbank>V01146</genbank>.
owned by: james
owned by: myers
part status: Released HQ 2013
mutable description: Transcription terminator for the E.coli RNA polymerase.
discontinued: false
dominant: false
experience: experience/Fails
group u list: _1_
m user id: 0
owner id: 24
owning group id: 7
sample status: In stock
status: status/Available
bookmark: false
mutable notes: 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). Use anywhere transcription should be stopped when the gene of interest is upstream of this terminator.
star: false
creator: Reshma Shetty
type: DnaRegion
role: SO:0000141
role: partType/Terminator
sequence annotation: BBa_B0012
sequence annotation: T7 TE
sequence annotation: polya
sequence annotation: stop
sequence: https://synbiohub.org/public/igem/BBa_B0012_sequence/1

BBa_B0012
type: SequenceAnnotation
persistent identity: annotation7020
display id: annotation7020
version: 1
top level: BBa_B0012
location: https://synbiohub.org/public/igem/BBa_B0012/annotation7020/range7020/1
role: feature/BioBrick
role: SO:0000804

https://synbiohub.org/public/igem/BBa_B0012/annotation7020/range7020/1
type: Range
persistent identity: range7020
display id: range7020
version: 1
top level: BBa_B0012
direction: direction/forward
start: 1
end: 41
orientation: inline

T7 TE
type: SequenceAnnotation
persistent identity: annotation1686
display id: annotation1686
version: 1
top level: BBa_B0012
location: https://synbiohub.org/public/igem/BBa_B0012/annotation1686/range1686/1
role: SO:0000313
role: feature/stem loop

https://synbiohub.org/public/igem/BBa_B0012/annotation1686/range1686/1
type: Range
persistent identity: range1686
display id: range1686
version: 1
top level: BBa_B0012
direction: direction/forward
start: 8
end: 27
orientation: inline

polya
type: SequenceAnnotation
persistent identity: annotation1690
display id: annotation1690
version: 1
top level: BBa_B0012
location: https://synbiohub.org/public/igem/BBa_B0012/annotation1690/range1690/1
role: feature/polya
role: SO:0000553

https://synbiohub.org/public/igem/BBa_B0012/annotation1690/range1690/1
type: Range
persistent identity: range1690
display id: range1690
version: 1
top level: BBa_B0012
direction: direction/forward
start: 28
end: 41
orientation: inline

stop
type: SequenceAnnotation
persistent identity: annotation1687
display id: annotation1687
version: 1
top level: BBa_B0012
location: https://synbiohub.org/public/igem/BBa_B0012/annotation1687/range1687/1
role: feature/stop
role: SO:0000319

https://synbiohub.org/public/igem/BBa_B0012/annotation1687/range1687/1
type: Range
persistent identity: range1687
display id: range1687
version: 1
top level: BBa_B0012
direction: direction/forward
start: 34
end: 34
orientation: inline

BBa_B0010
type: ComponentDefinition
persistent identity: BBa B0010
display id: BBa_B0010
version: 1
was generated by: iGEM to SBOL conversion
description: T1 from E. coli rrnB
created: 2003-11-19T12:00:00Z
modified: 2015-08-31T04:07:20Z
owned by: james
owned by: myers
mutable description: Transcriptional terminator consisting of a 64 bp stem-loop.
discontinued: false
dominant: false
experience: experience/None
group u list: _1_
m user id: 0
owner id: 24
owning group id: 7
sample status: In stock
status: status/Available
bookmark: false
star: true
creator: Randy Rettberg
type: DnaRegion
role: partType/Terminator
role: SO:0000141
sequence annotation: BBa_B0010
sequence annotation: stem_loop
sequence: https://synbiohub.org/public/igem/BBa_B0010_sequence/1

BBa_B0010
type: SequenceAnnotation
persistent identity: annotation7018
display id: annotation7018
version: 1
top level: BBa_B0010
location: https://synbiohub.org/public/igem/BBa_B0010/annotation7018/range7018/1
role: SO:0000804
role: feature/BioBrick

https://synbiohub.org/public/igem/BBa_B0010/annotation7018/range7018/1
type: Range
persistent identity: range7018
display id: range7018
version: 1
top level: BBa_B0010
direction: direction/forward
start: 1
end: 80
orientation: inline

stem_loop
type: SequenceAnnotation
persistent identity: annotation4184
display id: annotation4184
version: 1
top level: BBa_B0010
location: https://synbiohub.org/public/igem/BBa_B0010/annotation4184/range4184/1
role: feature/stem loop
role: SO:0000313

https://synbiohub.org/public/igem/BBa_B0010/annotation4184/range4184/1
type: Range
persistent identity: range4184
display id: range4184
version: 1
top level: BBa_B0010
direction: direction/forward
start: 12
end: 55
orientation: inline

BBa_B0030
type: ComponentDefinition
persistent identity: BBa B0030
display id: BBa_B0030
version: 1
was generated by: iGEM to SBOL conversion
description: RBS.1 (strong) -- modified from R. Weiss
created: 2003-01-31T12:00:00Z
modified: 2015-08-31T04:07:20Z
owned by: james
owned by: myers
part status: Released HQ 2013
mutable description: 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>.
discontinued: false
dominant: true
experience: experience/Works
group u list: _44_46_
m user id: 0
owner id: 24
owning group id: 7
sample status: In stock
status: status/Available
bookmark: false
mutable notes: Varies from -6 to +1 region from original sequence to accomodate BioBricks suffix ("orig" in figure 4-14 of Ron Weiss thesis). 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 Brian Chow
star: true
creator: Vinay S Mahajan, Voichita D. Marinescu, Brian Chow, Alexander D Wissner-Gross and Peter Carr IAP, 2003.
type: DnaRegion
role: SO:0000139
role: partType/RBS
sequence annotation: RBS-1\Strong
sequence annotation: BBa_B0030
sequence annotation: RBS
sequence: https://synbiohub.org/public/igem/BBa_B0030_sequence/1

RBS-1\Strong
type: SequenceAnnotation
persistent identity: annotation1701
display id: annotation1701
version: 1
top level: BBa_B0030
location: https://synbiohub.org/public/igem/BBa_B0030/annotation1701/range1701/1
role: SO:0000139
role: feature/rbs

https://synbiohub.org/public/igem/BBa_B0030/annotation1701/range1701/1
type: Range
persistent identity: range1701
display id: range1701
version: 1
top level: BBa_B0030
direction: direction/forward
start: 1
end: 15
orientation: inline

BBa_B0030
type: SequenceAnnotation
persistent identity: annotation7025
display id: annotation7025
version: 1
top level: BBa_B0030
location: https://synbiohub.org/public/igem/BBa_B0030/annotation7025/range7025/1
role: feature/BioBrick
role: SO:0000804

https://synbiohub.org/public/igem/BBa_B0030/annotation7025/range7025/1
type: Range
persistent identity: range7025
display id: range7025
version: 1
top level: BBa_B0030
direction: direction/forward
start: 1
end: 15
orientation: inline

RBS
type: SequenceAnnotation
persistent identity: annotation1702
display id: annotation1702
version: 1
top level: BBa_B0030
location: https://synbiohub.org/public/igem/BBa_B0030/annotation1702/range1702/1
role: feature/rbs
role: SO:0000139

https://synbiohub.org/public/igem/BBa_B0030/annotation1702/range1702/1
type: Range
persistent identity: range1702
display id: range1702
version: 1
top level: BBa_B0030
direction: direction/forward
start: 8
end: 12
orientation: inline

BBa_K352001
type: ComponentDefinition
persistent identity: BBa K352001
display id: BBa_K352001
version: 1
was generated by: iGEM to SBOL conversion
description: CooA from Rhodospirillum rubrum
created: 2010-10-01T11:00:00Z
modified: 2015-05-08T01:12:11Z
mutable provenance: 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.
owned by: james
owned by: myers
mutable description: 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.
discontinued: false
dominant: false
experience: experience/Works
group u list: _474_606_
m user id: 0
owner id: 5815
owning group id: 9
sample status: It's complicated
status: status/Planning
bookmark: true
mutable notes: The sequence information was acquired from NCBI and physical DNA was synthesized from GENEART. Classical cloning strategies(restriction digestion) were used to produce biobricks.
star: false
creator: Cihan Tastan
type: DnaRegion
role: SO:0000316
role: partType/Coding
sequence annotation: Start Codon
sequence: https://synbiohub.org/public/igem/BBa_K352001_sequence/1

Start Codon
type: SequenceAnnotation
persistent identity: annotation2081251
display id: annotation2081251
version: 1
top level: BBa_K352001
location: https://synbiohub.org/public/igem/BBa_K352001/annotation2081251/range2081251/1
role: feature/start
role: SO:0000318

https://synbiohub.org/public/igem/BBa_K352001/annotation2081251/range2081251/1
type: Range
persistent identity: range2081251
display id: range2081251
version: 1
top level: BBa_K352001
direction: direction/forward
start: 1
end: 3
orientation: inline

BBa_K352002
type: ComponentDefinition
persistent identity: BBa K352002
display id: BBa_K352002
version: 1
was generated by: iGEM to SBOL conversion
description: pCooF Promoter from Rhodospirillum rubrum
created: 2010-10-01T11:00:00Z
modified: 2015-05-08T01:12:11Z
mutable provenance: 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
owned by: james
owned by: myers
mutable description: 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.
discontinued: false
dominant: false
group u list: _474_
m user id: 0
owner id: 5815
owning group id: 9
sample status: It's complicated
status: status/Planning
bookmark: false
mutable notes: The sequence information was acquired from NCBI and physical DNA was synthesized from GENEART. Classical cloning strategies(restriction digestion) were used to produce biobricks.
star: false
creator: Ozkan IS
type: DnaRegion
role: partType/Regulatory
role: SO:0000167
sequence annotation: A+T rich sequence
sequence annotation: Protected by CooA+RNAP
sequence annotation: Protected by CooA
sequence annotation: CooA binding site
sequence annotation: -10 Region
sequence annotation: Transcription Start
sequence: https://synbiohub.org/public/igem/BBa_K352002_sequence/1

A+T rich sequence
type: SequenceAnnotation
persistent identity: annotation2081252
display id: annotation2081252
version: 1
top level: BBa_K352002
location: https://synbiohub.org/public/igem/BBa_K352002/annotation2081252/range2081252/1
role: feature/misc
role: SO:0000110

https://synbiohub.org/public/igem/BBa_K352002/annotation2081252/range2081252/1
type: Range
persistent identity: range2081252
display id: range2081252
version: 1
top level: BBa_K352002
direction: direction/forward
start: 8
end: 33
orientation: inline

Protected by CooA+RNAP
type: SequenceAnnotation
persistent identity: annotation2081258
display id: annotation2081258
version: 1
top level: BBa_K352002
location: https://synbiohub.org/public/igem/BBa_K352002/annotation2081258/range2081258/1
role: SO:0000330
role: feature/conserved

https://synbiohub.org/public/igem/BBa_K352002/annotation2081258/range2081258/1
type: Range
persistent identity: range2081258
display id: range2081258
version: 1
top level: BBa_K352002
direction: direction/forward
start: 23
end: 91
orientation: inline

Protected by CooA
type: SequenceAnnotation
persistent identity: annotation2081257
display id: annotation2081257
version: 1
top level: BBa_K352002
location: https://synbiohub.org/public/igem/BBa_K352002/annotation2081257/range2081257/1
role: SO:0000330
role: feature/conserved

https://synbiohub.org/public/igem/BBa_K352002/annotation2081257/range2081257/1
type: Range
persistent identity: range2081257
display id: range2081257
version: 1
top level: BBa_K352002
direction: direction/forward
start: 36
end: 61
orientation: inline

CooA binding site
type: SequenceAnnotation
persistent identity: annotation2081253
display id: annotation2081253
version: 1
top level: BBa_K352002
location: https://synbiohub.org/public/igem/BBa_K352002/annotation2081253/range2081253/1
role: feature/binding
role: SO:0001091

https://synbiohub.org/public/igem/BBa_K352002/annotation2081253/range2081253/1
type: Range
persistent identity: range2081253
display id: range2081253
version: 1
top level: BBa_K352002
direction: direction/forward
start: 41
end: 44
orientation: inline

CooA binding site
type: SequenceAnnotation
persistent identity: annotation2081254
display id: annotation2081254
version: 1
top level: BBa_K352002
location: https://synbiohub.org/public/igem/BBa_K352002/annotation2081254/range2081254/1
role: SO:0001091
role: feature/binding

https://synbiohub.org/public/igem/BBa_K352002/annotation2081254/range2081254/1
type: Range
persistent identity: range2081254
display id: range2081254
version: 1
top level: BBa_K352002
direction: direction/forward
start: 52
end: 56
orientation: inline

-10 Region
type: SequenceAnnotation
persistent identity: annotation2081255
display id: annotation2081255
version: 1
top level: BBa_K352002
location: https://synbiohub.org/public/igem/BBa_K352002/annotation2081255/range2081255/1
role: SO:0000110
role: feature/misc

https://synbiohub.org/public/igem/BBa_K352002/annotation2081255/range2081255/1
type: Range
persistent identity: range2081255
display id: range2081255
version: 1
top level: BBa_K352002
direction: direction/forward
start: 79
end: 84
orientation: inline

Transcription Start
type: SequenceAnnotation
persistent identity: annotation2081256
display id: annotation2081256
version: 1
top level: BBa_K352002
location: https://synbiohub.org/public/igem/BBa_K352002/annotation2081256/range2081256/1
role: feature/start
role: SO:0000318

https://synbiohub.org/public/igem/BBa_K352002/annotation2081256/range2081256/1
type: Range
persistent identity: range2081256
display id: range2081256
version: 1
top level: BBa_K352002
direction: direction/forward
start: 92
end: 93
orientation: inline

amilCP
type: ComponentDefinition
persistent identity: BBa K592009
display id: BBa_K592009
version: 1
was generated by: iGEM to SBOL conversion
description: amilCP, blue chromoprotein
created: 2011-09-17T11:00:00Z
modified: 2015-05-08T01:12:48Z
mutable provenance: Acropora millepora
owned by: james
owned by: myers
part status: Released HQ 2013
mutable description: 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).
discontinued: false
dominant: false
experience: experience/Works
group u list: _763_
m user id: 0
owner id: 7929
owning group id: 9
sample status: In stock
status: status/Available
bookmark: true
mutable notes: Illegal internal restriction site had to be removed (EcoRI).
star: false
creator: Lei Sun
type: DnaRegion
role: partType/Coding
role: SO:0000316
sequence annotation: amilCP
sequence: https://synbiohub.org/public/igem/BBa_K592009_sequence/1

amilCP
type: SequenceAnnotation
persistent identity: annotation2131628
display id: annotation2131628
version: 1
top level: amilCP
location: https://synbiohub.org/public/igem/BBa_K592009/annotation2131628/range2131628/1
role: SO:0000316
role: feature/cds

https://synbiohub.org/public/igem/BBa_K592009/annotation2131628/range2131628/1
type: Range
persistent identity: range2131628
display id: range2131628
version: 1
top level: amilCP
direction: direction/forward
start: 1
end: 666
orientation: inline

spacer
type: ComponentDefinition
persistent identity: BBa B0040
display id: BBa_B0040
version: 1
was generated by: iGEM to SBOL conversion
description: Spacer.1 (generic)
created: 2003-01-31T12:00:00Z
modified: 2015-08-31T04:07:20Z
mutable provenance: Randomly generated and optimized for several parameters (see Design notes).
owned by: james
owned by: myers
part status: Released HQ 2013
mutable description: 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.
discontinued: false
dominant: false
experience: experience/Works
group u list: _1_
m user id: 0
owner id: 24
owning group id: 7
sample status: In stock
status: status/Available
bookmark: false
mutable notes: 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 Random DNA Generator 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 E.coli 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. 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): T->A @ 85 T->A @ 42 C->T @ 79 A->T @ 64 A->T @ 31 T->A @ 34 C->A @ 37 Also, note that the above changes further reduce (the already very weak) homology to current NCBI-stored sequences. 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. The sequence is compatible (does not show significant homology) with the components in the Elowitz repressilator plasmid.
star: true
creator: Vinay S. Mahajan, Brian Chow, Peter Carr
type: DnaRegion
role: partType/DNA
role: SO:0000110
sequence annotation: Spacer-1
sequence annotation: BBa_B0040
sequence: https://synbiohub.org/public/igem/BBa_B0040_sequence/1

Spacer-1
type: SequenceAnnotation
persistent identity: annotation1721
display id: annotation1721
version: 1
top level: spacer
location: https://synbiohub.org/public/igem/BBa_B0040/annotation1721/range1721/1
role: feature/misc
role: SO:0000110

https://synbiohub.org/public/igem/BBa_B0040/annotation1721/range1721/1
type: Range
persistent identity: range1721
display id: range1721
version: 1
top level: spacer
direction: direction/forward
start: 1
end: 70
orientation: inline

BBa_B0040
type: SequenceAnnotation
persistent identity: annotation7030
display id: annotation7030
version: 1
top level: spacer
location: https://synbiohub.org/public/igem/BBa_B0040/annotation7030/range7030/1
role: feature/BioBrick
role: SO:0000804

https://synbiohub.org/public/igem/BBa_B0040/annotation7030/range7030/1
type: Range
persistent identity: range7030
display id: range7030
version: 1
top level: spacer
direction: direction/forward
start: 1
end: 70
orientation: inline

BBa_J23110
type: ComponentDefinition
persistent identity: BBa J23110
display id: BBa_J23110
version: 1
was generated by: iGEM to SBOL conversion
description: constitutive promoter family member
created: 2006-08-16T11:00:00Z
modified: 2015-08-31T04:08:40Z
mutable provenance: Later
owned by: james
owned by: myers
mutable description: Later
discontinued: false
dominant: true
experience: experience/Works
group u list: _52_
m user id: 0
owner id: 483
owning group id: 95
sample status: In stock
status: status/Available
bookmark: true
mutable notes: N/A
star: true
creator: John Anderson
type: DnaRegion
role: SO:0000167
role: partType/Regulatory
sequence: https://synbiohub.org/public/igem/BBa_J23110_sequence/1

https://synbiohub.org/public/igem/BBa_K2056003_sequence/1
type: Sequence
persistent identity: BBa K2056003 sequence
display id: BBa_K2056003_sequence
version: 1
was generated by: iGEM to SBOL conversion
owned by: james
owned by: myers
elements: tttacggctagctcagtcctaggtacaatgctagctactagagattaaagaggagaaatactagatgccaccacgcttcaatattgcaaacgtactgctgtctcctgatggtgagacgttcttccgcggttttcgctctaagattcatgcgaaaggctctctggtatgtactggtgaaggtgatgaaaacggtgtttttgttgtggttgatggtcgcctgcgtgtttacctggttggtgaggagcgtgagattagcctgttctacctgacttccggcgatatgttctgcatgcattccggctgcctggttgaagccaccgagcgcaccgaagtgcgtttcgccgatatccgcacgttcgagcagaaactgcaaacctgtccgtctatggcatggggcctgatcgccattctgggccgtgctctgacctcctgtatgcgtaccatcgaagacctgatgttccacgatattaaacaacgtatcgcgggctttttcatcgaccacgctaacactaccggtcgccagactcagggtggcgtaattgtttctgttgacttcactgtagaggaaatcgctaatctgatcggtagctcccgccagactactagcacggcgctgaactctctgattaaagagggttacatctcccgccagggccgtggtcactatactatcccgaacctggttcgcctgaaggcggctgcggatggtgaccgcgatgacgatgacgattgatactagagccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctctactagagaggttctgttaagtaactgaacccaatgtcgttagtgacgcttacctcttaagaggtcactgacctaacatactagagttcggcgtcttttcatacccccataaaaactctggataactgtcatctggccgacagacggggccgggctttttgtcgcttactcggcgccaggtactagagattaaagaggagaaatactagatgagtgtgatcgctaaacaaatgacctacaaggtttatatgtcaggcacggtcaatggacactactttgaggtcgaaggcgatggaaaaggtaagccctacgagggggagcagacggtaaagctcactgtcaccaagggcggacctctgccatttgcttgggatattttatcaccacagtgtcagtacggaagcataccattcaccaagtaccctgaagacatccctgactatgtaaagcagtcattcccggagggctatacatgggagaggatcatgaactttgaagatggtgcagtgtgtactgtcagcaatgattccagcatccaaggcaactgtttcatctaccatgtcaagttctctggtttgaactttcctcccaatggacctgtcatgcagaagaagacacagggctgggaacccaacactgagcgtctctttgcacgagatggaatgctgctaggaaacaactttatggctctgaagttagaaggaggcggtcactatttgtgtgaatttaaaactacttacaaggcaaagaagcctgtgaagatgccagggtatcactatgttgaccgcaaactggatgtaaccaatcacaacaaggattacacttcggttgagcagtgtgaaatttccattgcacgcaaacctgtggtcgcctaataatactagagtcacactggctcaccttcgggtgggcctttctgcgtttata
encoding: naseq.html

https://synbiohub.org/public/igem/BBa_B0012_sequence/1
type: Sequence
persistent identity: BBa B0012 sequence
display id: BBa_B0012_sequence
version: 1
was generated by: iGEM to SBOL conversion
owned by: james
owned by: myers
elements: tcacactggctcaccttcgggtgggcctttctgcgtttata
encoding: naseq.html

https://synbiohub.org/public/igem/BBa_B0010_sequence/1
type: Sequence
persistent identity: BBa B0010 sequence
display id: BBa_B0010_sequence
version: 1
was generated by: iGEM to SBOL conversion
owned by: james
owned by: myers
elements: ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtgaacgctctc
encoding: naseq.html

https://synbiohub.org/public/igem/BBa_B0030_sequence/1
type: Sequence
persistent identity: BBa B0030 sequence
display id: BBa_B0030_sequence
version: 1
was generated by: iGEM to SBOL conversion
owned by: james
owned by: myers
elements: attaaagaggagaaa
encoding: naseq.html

https://synbiohub.org/public/igem/BBa_K352001_sequence/1
type: Sequence
persistent identity: BBa K352001 sequence
display id: BBa_K352001_sequence
version: 1
was generated by: iGEM to SBOL conversion
owned by: james
owned by: myers
elements: atgccaccacgcttcaatattgcaaacgtactgctgtctcctgatggtgagacgttcttccgcggttttcgctctaagattcatgcgaaaggctctctggtatgtactggtgaaggtgatgaaaacggtgtttttgttgtggttgatggtcgcctgcgtgtttacctggttggtgaggagcgtgagattagcctgttctacctgacttccggcgatatgttctgcatgcattccggctgcctggttgaagccaccgagcgcaccgaagtgcgtttcgccgatatccgcacgttcgagcagaaactgcaaacctgtccgtctatggcatggggcctgatcgccattctgggccgtgctctgacctcctgtatgcgtaccatcgaagacctgatgttccacgatattaaacaacgtatcgcgggctttttcatcgaccacgctaacactaccggtcgccagactcagggtggcgtaattgtttctgttgacttcactgtagaggaaatcgctaatctgatcggtagctcccgccagactactagcacggcgctgaactctctgattaaagagggttacatctcccgccagggccgtggtcactatactatcccgaacctggttcgcctgaaggcggctgcggatggtgaccgcgatgacgatgacgattga
encoding: naseq.html

https://synbiohub.org/public/igem/BBa_K352002_sequence/1
type: Sequence
persistent identity: BBa K352002 sequence
display id: BBa_K352002_sequence
version: 1
was generated by: iGEM to SBOL conversion
owned by: james
owned by: myers
elements: ttcggcgtcttttcatacccccataaaaactctggataactgtcatctggccgacagacggggccgggctttttgtcgcttactcggcgccagg
encoding: naseq.html

https://synbiohub.org/public/igem/BBa_K592009_sequence/1
type: Sequence
persistent identity: BBa K592009 sequence
display id: BBa_K592009_sequence
version: 1
was generated by: iGEM to SBOL conversion
owned by: james
owned by: myers
elements: atgagtgtgatcgctaaacaaatgacctacaaggtttatatgtcaggcacggtcaatggacactactttgaggtcgaaggcgatggaaaaggtaagccctacgagggggagcagacggtaaagctcactgtcaccaagggcggacctctgccatttgcttgggatattttatcaccacagtgtcagtacggaagcataccattcaccaagtaccctgaagacatccctgactatgtaaagcagtcattcccggagggctatacatgggagaggatcatgaactttgaagatggtgcagtgtgtactgtcagcaatgattccagcatccaaggcaactgtttcatctaccatgtcaagttctctggtttgaactttcctcccaatggacctgtcatgcagaagaagacacagggctgggaacccaacactgagcgtctctttgcacgagatggaatgctgctaggaaacaactttatggctctgaagttagaaggaggcggtcactatttgtgtgaatttaaaactacttacaaggcaaagaagcctgtgaagatgccagggtatcactatgttgaccgcaaactggatgtaaccaatcacaacaaggattacacttcggttgagcagtgtgaaatttccattgcacgcaaacctgtggtcgcctaataa
encoding: naseq.html

https://synbiohub.org/public/igem/BBa_B0040_sequence/1
type: Sequence
persistent identity: BBa B0040 sequence
display id: BBa_B0040_sequence
version: 1
was generated by: iGEM to SBOL conversion
owned by: james
owned by: myers
elements: aggttctgttaagtaactgaacccaatgtcgttagtgacgcttacctcttaagaggtcactgacctaaca
encoding: naseq.html

https://synbiohub.org/public/igem/BBa_J23110_sequence/1
type: Sequence
persistent identity: BBa J23110 sequence
display id: BBa_J23110_sequence
version: 1
was generated by: iGEM to SBOL conversion
owned by: james
owned by: myers
elements: tttacggctagctcagtcctaggtacaatgctagc
encoding: naseq.html

iGEM to SBOL conversion
type: Activity
persistent identity: igem2sbol
display id: igem2sbol
version: 1
description: Conversion of the iGEM parts registry to SBOL2.1
owned by: james
owned by: myers
creator: James Alastair McLaughlin
creator: Chris J. Myers
ended at time: 2017-03-06T15:00:00.000Z