Coding

Part:BBa_K1981007

Designed by: Yulei Dang   Group: iGEM16_NKU_China   (2016-10-14)
Revision as of 14:44, 14 October 2016 by Songxinhao (Talk | contribs) (→‎Protein-Data Table)


mtn

S-ribosylhomocysteine lyase. Involved in the synthesis of autoinducer 2 (AI-2) which is secreted by bacteria and is used to communicate both the cell density and the metabolic potential of the environment. The regulation of gene expression in response to changes in cell density is called quorum sensing. Catalyzes the transformation of S-ribosylhomocysteine (RHC) to homocysteine (HC) and 4,5-dihydroxy-2,3-pentadione (DPD).

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
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 475
  • 1000
    COMPATIBLE WITH RFC[1000]


Usage and Biology

The AI-2 “supplier” was constructed by overexpressing the luxS gene.

This part was originated from Bacillus amyloliquefaciens LL3.

Characterization

Protein-Data Table

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 10: (underlined part encodes the protein)
 ATGAAAATC ... GCACATGGCTAA
 ORF from nucleotide position 1 to 696 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 		MKIGIIGAMEEEVTLLRDKIENRQTISLGGCEIYTGQLNGTEVALLKSGIGKVAAALGATLLLEHCKPDVIINTGSAGGLAPTLKVGDIVVSDEARYHDA
DVTAFGYEYGQLPGCPAGFKADDKLIAAAEACIAELNLNAVRGLIVSGDAFINGSVGLAKIRHNFPQAIAVEMEATAIAHVCHNFNVPFVVVRAISDVAD
QQSHLSFDEFLAVAAKQSSLMVESLVQKLAHG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
RFC25 scar (shown in bold): 35 to 36
Amino acid composition:
Ala (A)32 (13.8%)
Arg (R)6 (2.6%)
Asn (N)9 (3.9%)
Asp (D)12 (5.2%)
Cys (C)5 (2.2%)
Gln (Q)8 (3.4%)
Glu (E)15 (6.5%)
Gly (G)22 (9.5%)
His (H)7 (3.0%)
Ile (I)18 (7.8%)
Leu (L)23 (9.9%)
Lys (K)11 (4.7%)
Met (M)4 (1.7%)
Phe (F)8 (3.4%)
Pro (P)6 (2.6%)
Ser (S)12 (5.2%)
Thr (T)9 (3.9%)
Trp (W)0 (0.0%)
Tyr (Y)4 (1.7%)
Val (V)21 (9.1%)
Amino acid counting
Total number:232
Positively charged (Arg+Lys):17 (7.3%)
Negatively charged (Asp+Glu):27 (11.6%)
Aromatic (Phe+His+Try+Tyr):19 (8.2%)
Biochemical parameters
Atomic composition:C1079H1738N292O329S9
Molecular mass [Da]:24354.0
Theoretical pI:5.09
Extinction coefficient at 280 nm [M-1 cm-1]:5960 / 6273 (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):excellent (0.82)excellent (0.81)good (0.63)good (0.68)good (0.80)good (0.70)
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)
Subcellular Localization (reliability in brackets)
Archaea: -
Bacteria: -
Eukarya: -
Gene Ontology (reliability in brackets)
Molecular Function Ontology:0005515 0. (NaN%), 0004731 0. (NaN%)
Biological Process Ontology:0009164 0. (NaN%), 0009086 0. (NaN%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
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.

[edit]
Categories
Parameters
None