Coding

Part:BBa_K1981001

Designed by: Yulei Dang, Xinhao Song   Group: iGEM16_NKU_China   (2016-10-14)
Revision as of 16:45, 14 October 2016 by Songxinhao (Talk | contribs) (→‎Characterization)


lsrA

Autoinducer 2 import ATP-binding protein LsrA. 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. Responsible for energy coupling to the transport system (Probable). This protein is essential for aerobic growth. 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

The colony PCR verification result for lsrA is shown in Figure 1.

alt text

Protein-Data Table

Protein data table for BioBrick BBa_K1981001 automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGACGATA ... GTAGCGGAATGA
 ORF from nucleotide position 1 to 1197 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 		MTIEENICIGLKEKKKKLKVQIQQLISSLGWDIALNKLGGTLSIAQQQLVEIVRGLIREAEILILDEPTSTLTTHEIKSLFVLMKSLQEKGIGMIYITHR
FPEIFEIANKVAILRDGMVVSQGDVCDYTYDMLMEGLLPKGYKQKEKIEVVQETAKTKKILEVVDINGHAFENISFTVHAGEVVGVAGIIGSGRTELAEA
IFGLKAIKSGSILLEGKSIDTCSLHKRLSEGLVYVPEDRARNGIFSIASVKENIAAATSLYQNNRFFINQEKESALVNSFIEQFRIVVQNMNKELASLSG
GNQQKVVLAKYLACNPKIIILDEPTRGIDAKARLEVYETIKKMKREGLAILLISSDVEEIVQLVNRVYVMRNGRFVSHMEKEQLSVNEVTRLAYGGVAE*
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)26 (6.5%)
Arg (R)17 (4.3%)
Asn (N)18 (4.5%)
Asp (D)12 (3.0%)
Cys (C)4 (1.0%)
Gln (Q)18 (4.5%)
Glu (E)38 (9.5%)
Gly (G)29 (7.3%)
His (H)6 (1.5%)
Ile (I)42 (10.5%)
Leu (L)41 (10.3%)
Lys (K)33 (8.3%)
Met (M)10 (2.5%)
Phe (F)12 (3.0%)
Pro (P)6 (1.5%)
Ser (S)25 (6.3%)
Thr (T)17 (4.3%)
Trp (W)1 (0.3%)
Tyr (Y)10 (2.5%)
Val (V)34 (8.5%)
Amino acid counting
Total number:399
Positively charged (Arg+Lys):50 (12.5%)
Negatively charged (Asp+Glu):50 (12.5%)
Aromatic (Phe+His+Try+Tyr):29 (7.3%)
Biochemical parameters
Atomic composition:C1984H3262N532O588S14
Molecular mass [Da]:44425.8
Theoretical pI:7.03
Extinction coefficient at 280 nm [M-1 cm-1]:20400 / 20650 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.70)good (0.74)good (0.66)good (0.75)good (0.77)good (0.66)
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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Categories
Parameters
None