Difference between revisions of "Part:BBa K1981004"

Latest revision as of 01:41, 15 October 2016

lsrD

Autoinducer 2 import system permease protein LsrD. Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. It's responsible for regulation of uptake and processing of the quorum-sensing AI-2 and it is probably responsible for the translocation of the substrate across the membrane. Share the same promoter with lsrA. It shares the same promoter with lsrA. In the absence of AI-2, it is repressed by LsrR. It can be induced by AI-2, via releasing of the LsrR repressor. In the absence of glucose, it was induced by cAMP-CRP by direct binding to the upstream region of the lsr promoter.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

Usage and Biology

AI-2 “Consumer” was constructed by overexpressing the lsrACDB gene in Bacillus amyloliquefaciens LL3.

This part is originated from Bacillus thuringiensis serovar thuringiensis str. IS5056.

Characterization

The restriction enzyme digestion verification result for lsrD is shown in Figure 1.

Figure 1: Restriction Enzyme Digestion Verification for lsrD

Protein-Data Table

Protein data table for BioBrick BBa_K1981004 automatically created by the BioBrick-AutoAnnotator version 1.0

Nucleotide sequence in RFC 10: (underlined part encodes the protein)
ATGAAGTAT ... GAAATGTCATGA
ORF from nucleotide position 1 to 987 (excluding stop-codon)

Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

1
101
201
301

MKYLYRWEGVLIVLLLIEFILFSFINSDFLNISNLLFSTNDFLFIAIAAIPMTFVIVTGGIDVSVGSIMGLTSILIGVLWMNGIPILFAVIIALIISCLA
GALNGLIIKMTDVEPLVVTLGTMFLYGGIALVISGGAGASGYEGISGLPDTYVQLANGSFIGIPNLLWLLISLTIVYTILFHRTIYGRYVKLTGANENTA
KYTGIKTKKVVIIAYILSGLGGGLGGVFLTAYFGSARADIGSETILPIITAVVLGGTLITGGKGSIFGTVLASIFIGLMQYGLQMTGLTNEQSNVVIGII
LILSVIMRHFKLHQFLAGKRQSWHKGEMS*

Sequence features: (with their position in the amino acid sequence, see the list of supported features)

None of the supported features appeared in the sequence

Amino acid composition:

Ala (A)	20 (6.1%)
Arg (R)	6 (1.8%)
Asn (N)	12 (3.6%)
Asp (D)	6 (1.8%)

Cys (C)	1 (0.3%)
Gln (Q)	6 (1.8%)
Glu (E)	8 (2.4%)
Gly (G)	43 (13.1%)

His (H)	4 (1.2%)
Ile (I)	47 (14.3%)
Leu (L)	46 (14.0%)
Lys (K)	11 (3.3%)

Met (M)	10 (3.0%)
Phe (F)	18 (5.5%)
Pro (P)	6 (1.8%)
Ser (S)	22 (6.7%)

Thr (T)	23 (7.0%)
Trp (W)	4 (1.2%)
Tyr (Y)	12 (3.6%)
Val (V)	24 (7.3%)

Amino acid counting

	Total number:	329
	Positively charged (Arg+Lys):	17 (5.2%)
	Negatively charged (Asp+Glu):	14 (4.3%)
	Aromatic (Phe+His+Try+Tyr):	38 (11.6%)

Biochemical parameters

	Atomic composition:	C₁₆₄₇H₂₆₂₆N₃₈₈O₄₃₃S₁₁
	Molecular mass [Da]:	35144.0
	Theoretical pI:	8.87
	Extinction coefficient at 280 nm [M^-1 cm^-1]:	39880 / 39943 (all Cys red/ox)

Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges

Codon usage

	Organism:	E. coli	B. subtilis	S. cerevisiae	A. thaliana	P. patens	Mammals
	Codon quality (CAI):	good (0.68)	good (0.73)	good (0.69)	good (0.75)	good (0.69)	acceptable (0.55)

Alignments (obtained from PredictProtein.org)
There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.

Predictions (obtained from PredictProtein.org)

There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours.

The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
If you have any questions, comments or suggestions, please leave us a comment.

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 <partinfo>BBa_K1981004 short</partinfo>
-Autoinducer 2 import system permease protein LsrD. Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. Regulation of uptake and processing of the quorum-sensing AI-2. Probably responsible for the translocation of the substrate across the membrane. Share the same promoter with <i>lsrA</i>. In the absence of AI-2, repressed by LsrR. Induced by AI-2, via release of the LsrR repressor. In the absence of glucose, induced by cAMP-CRP by direct binding to the upstream region of the <i>lsr</i> promoter.
+Autoinducer 2 import system permease protein LsrD. Part of the ABC transporter complex LsrABCD involved in autoinducer 2 (AI-2) import. It's responsible for regulation of uptake and processing of the quorum-sensing AI-2 and it is probably responsible for the translocation of the substrate across the membrane. Share the same promoter with <i>lsrA</i>. It shares the same promoter with lsrA. In the absence of AI-2, it is repressed by LsrR. It can be induced by AI-2, via releasing of the LsrR repressor. In the absence of glucose, it was induced by cAMP-CRP by direct binding to the upstream region of the lsr promoter.
 <!-- Add more about the biology of this part here