Coding

Part:BBa_K1981004

Designed by: Yulei Dang, Xinhao Song   Group: iGEM16_NKU_China   (2016-10-14)
Revision as of 01:41, 15 October 2016 by MengFankang Nankai (Talk | contribs)

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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. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
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.
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Categories
Parameters
None