Part:BBa_K1471005

AGS (Linker) - VP16 (Activation domain).

For this part, we fused the nine base pairs AGS linker subbmited by iGEM13_Freiburg and the Transactivation domain from the VP16 protein from the Herpes Simplex Virus, submitted by iGEM08_ESBS-Strasbourg.

AGS linker is a small sequence of aminoacids (3 aa). Its name is derived from the aminoacids components of its chain, which are Alanine (A), Glycine (G) and Serine (S). It's widely used for fusing proteins domains in Tandem-like synthetic constructs.

VP16 is a transcription factor from Herpes simplex virus that activates the transcription of some viral late genes. In synthetic constructions, VP16 activation domain has probed to be effective at activating the expression of some genes when fused to an adecuate DNA-Binding domain.

This part may be useful to simplify the designing of synthetic constructs intended to be used in eucaryotic cells.

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]

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)  GCAGGCTCCTACTAGAGGCGCGTACGAAAAACAATTACGGGTCTACCATCGAGGGCCTGCTCGATCTCCCGGACGACGACGCCCCCGAAGAGGCGGGGCTGGCGGCTCCGCGCCTGTCCTTTCTCCCCGCGGGACACACGCGCAGACTGTCGACGGCCCCCCCGACCGATGTCAGCC ... AGCTCCACTTAGACGGCGAGGACGTGGCGATGGCGCATGCCGACGCGCTAGACGATTTCGATCTGGACATGTTGGGGGACGGGGATTCCCCGGGTCCGGGATTTACCCCCCACGACTCCGCCCCCTACGGCGCTCTGGATATGGCCGACTTCGAGTTTGAGCAGATGTTTACCGATGCCCTTGGAATTGACGAGTACGGTGGG  ORF from nucleotide position 169 to 195 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below) 1  MSAWGTSST*
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) 1 (11.1%) Arg (R) 0 (0.0%) Asn (N) 0 (0.0%) Asp (D) 0 (0.0%) Cys (C) 0 (0.0%) Gln (Q) 0 (0.0%) Glu (E) 0 (0.0%) Gly (G) 1 (11.1%) His (H) 0 (0.0%) Ile (I) 0 (0.0%) Leu (L) 0 (0.0%) Lys (K) 0 (0.0%) Met (M) 1 (11.1%) Phe (F) 0 (0.0%) Pro (P) 0 (0.0%) Ser (S) 3 (33.3%) Thr (T) 2 (22.2%) Trp (W) 1 (11.1%) Tyr (Y) 0 (0.0%) Val (V) 0 (0.0%)
Amino acid counting Total number: 9 Positively charged (Arg+Lys): 0 (0.0%) Negatively charged (Asp+Glu): 0 (0.0%) Aromatic (Phe+His+Try+Tyr): 1 (11.1%)	Biochemical parameters Atomic composition: C38H58N10O15S1 Molecular mass [Da]: 927.0 Theoretical pI: 5.28 Extinction coefficient at 280 nm [M-1 cm-1]: 5500 / 5500 (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 (0.77) good (0.66) acceptable (0.53) acceptable (0.52) excellent (0.80) good (0.69)
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. If you have any questions, comments or suggestions, please leave us a comment.