Difference between revisions of "Part:BBa K1981002"

Revision as of 14:29, 14 October 2016

lsrB

Autoinducer 2-binding protein LsrB. Membrane channel protein. 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. Binds AI-2 and delivers it to the LsrC and LsrD permeases (Probable). Share the same promoter with lsrA. 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 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

Protein-Data Table

Protein data table for BioBrick BBa_K1981002 automatically created by the BioBrick-AutoAnnotator version 1.0

Nucleotide sequence in RFC 10: (underlined part encodes the protein)
ATGAAGAGA ... TATAATTTTTAG
ORF from nucleotide position 1 to 1041 (excluding stop-codon)

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

1
101
201
301

MKRKLGIVLIVCICLIGLIACSSQTADKKKADDVKFAFIPKLTGVGFFTSGGEGAKEMGDKLGVQVKYDGPSEASVSGQVKYINNFINQNYDALMVSSTS
VDGLSQSLQRAKKKGMTVLTWDSDVNPKDRSFYISQGTPDQLANLLIEMTSKQIGDKGKVAFFYSSPTVTDQNQWVTKAKEIIKKKYPNWEIVTTQYGEN
NAQKSLSVGENILKTYPDINAVICPDATALPAMAQAAENLKMDKKVVVTGFSTPNVMRDYVKRGTVQQFGLWDVKQQGALATYVANEIVVKGKKLKVGDS
FEVKGIGKVKVEPNSIQGYDYEAEGNGIIVLPERVVFTKDNIDKYNF*

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)	23 (6.6%)
Arg (R)	6 (1.7%)
Asn (N)	19 (5.5%)
Asp (D)	22 (6.3%)

Cys (C)	4 (1.2%)
Gln (Q)	19 (5.5%)
Glu (E)	15 (4.3%)
Gly (G)	29 (8.4%)

His (H)	0 (0.0%)
Ile (I)	23 (6.6%)
Leu (L)	21 (6.1%)
Lys (K)	39 (11.2%)

Met (M)	8 (2.3%)
Phe (F)	13 (3.7%)
Pro (P)	12 (3.5%)
Ser (S)	22 (6.3%)

Thr (T)	20 (5.8%)
Trp (W)	4 (1.2%)
Tyr (Y)	13 (3.7%)
Val (V)	35 (10.1%)

Amino acid counting

	Total number:	347
	Positively charged (Arg+Lys):	45 (13.0%)
	Negatively charged (Asp+Glu):	37 (10.7%)
	Aromatic (Phe+His+Try+Tyr):	30 (8.6%)

Biochemical parameters

	Atomic composition:	C₁₇₀₆H₂₇₂₄N₄₄₆O₅₁₅S₁₂
	Molecular mass [Da]:	38107.8
	Theoretical pI:	9.02
	Extinction coefficient at 280 nm [M^-1 cm^-1]:	41370 / 41620 (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 (0.75)	good (0.79)	good (0.73)	good (0.76)	good (0.72)	acceptable (0.59)

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.

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@@ Line 18: / Line 18: @@
 <!-- -->
 ===Usage and Biology===
-AI-2 “Consumer” was constructed by overexpressing the <i>lsrACDB</i>, <i>lsrFG</i> and <i>lsrK</i> genes in <i>Bacillus amyloliquefaciens LL3</i>.
+AI-2 “Consumer” was constructed by overexpressing the <i>lsrACDB</i> gene in <i>Bacillus amyloliquefaciens LL3</i>.
 <div>This part is originated from <i>Bacillus thuringiensis</i> serovar thuringiensis str. IS5056.</div>