Coding

Part:BBa_K1981006

Designed by: Yulei Dang   Group: iGEM16_NKU_China   (2016-10-14)
Revision as of 14:36, 14 October 2016 by Songxinhao (Talk | contribs) (→‎Protein-Data Table)


lsrK

Autoinducer-2 kinase. Catalyzes the phosphorylation of autoinducer-2 (AI-2) to phospho-AI-2, which subsequently inactivates the transcriptional regulator LsrR and leads to the transcription of the lsr operon. Phosphorylates the ring-open form of (S)-4,5-dihydroxypentane-2,3-dione (DPD), which is the precursor to all AI-2 signaling molecules, at the C5 position. Required for the regulation of the lsr operon and many other genes.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 555
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 229
  • 1000
    COMPATIBLE WITH RFC[1000]


Usage and Biology

AI-2 “Consumer” was constructed by overexpressing the lsrK gene.

This part is originated from Escherichia coli strain K12.

Characterizaion

Protein-Data Table

Protein data table for BioBrick BBa_K1981006 automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGGCTCGA ... CCTGGGTTATAG
 ORF from nucleotide position 1 to 1590 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 
301 
401 
501 		MARLFTPSESKYYLMALDAGTGSIRAVIFDLEGNQIAVGQAEWRHLAVPDVPGSMEFDLNKNWQLACECMRQALHNAGIAPEYIAAVSACSMREGIVLYN
NEGTPIWACANVDARAAREVSELKELHNNTFENEVYRATGQTLALSAIPRLLWLAHHRSDIYRQASTITMISDWLAYMLSGELAVDPSNAGTTGLLDLTT
RDWKPALLDMAGLRADILSPVKETGTLLGVVSSQAAELCGLKAGTPVVVGGGDVQLGCLGLGVVRPAQTAVLGGTFWQQVVNLAAPVTDPEMNVRVNPHV
IPGMVQAESISFFTGLTMRWFRDAFCAEEKLIAERLGIDTYTLLEEMASRVPPGSWGVMPIFSDRMRFKTWYHAAPSFINLSIDPDKCNKATLFRALEEN
AAIVSACNLQQIADFSNIHPSSLVFAGGGSKGKLWSQILADVSGLPVNIPVVKEATALGCAIAAGVGAGIFSSMAETGERLVRWERTHTPDPEKHELYQD
SRDKWQAVYQDQLGLVDHGLTTSLWKAPGL*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
RFC25 scar (shown in bold): 224 to 225
Amino acid composition:
Ala (A)61 (11.5%)
Arg (R)26 (4.9%)
Asn (N)20 (3.8%)
Asp (D)26 (4.9%)
Cys (C)10 (1.9%)
Gln (Q)19 (3.6%)
Glu (E)31 (5.8%)
Gly (G)43 (8.1%)
His (H)11 (2.1%)
Ile (I)26 (4.9%)
Leu (L)56 (10.6%)
Lys (K)16 (3.0%)
Met (M)15 (2.8%)
Phe (F)16 (3.0%)
Pro (P)26 (4.9%)
Ser (S)34 (6.4%)
Thr (T)30 (5.7%)
Trp (W)14 (2.6%)
Tyr (Y)11 (2.1%)
Val (V)39 (7.4%)
Amino acid counting
Total number:530
Positively charged (Arg+Lys):42 (7.9%)
Negatively charged (Asp+Glu):57 (10.8%)
Aromatic (Phe+His+Try+Tyr):52 (9.8%)
Biochemical parameters
Atomic composition:C2562H4019N699O759S25
Molecular mass [Da]:57558.8
Theoretical pI:5.25
Extinction coefficient at 280 nm [M-1 cm-1]:93390 / 94015 (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 (0.78)good (0.80)acceptable (0.60)good (0.66)good (0.77)good (0.65)
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