Coding

Part:BBa_K1159301

Designed by: Dong-Jiunn Jeffery TRUONG   Group: iGEM13_TU-Munich   (2013-09-14)
Revision as of 20:50, 8 October 2013 by JohannaB (Talk | contribs)

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Super Yellow Fluorescent Protein 2 (SYFP2) in RFC[25]

Improved part of BBa_K864100 which originally cannot be fused to other protein domains. This improved version is flanked by RFC[25] pre- and suffix for further protein fusions.

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 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)
 ATGGCCGGCGTTAGCAAG ... CTGTATAAAACCGGT
 ORF from nucleotide position -8 to 720 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 
201 		MAGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKLICTTGKLPVPWPTLVTTLGYGVQCFARYPDHMKQHDFFKSAMPEGYVQERT
IFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGGVQLADHYQQNTPIGDGPVLLPD
NHYLSYQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKTG*
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)10 (4.1%)
Arg (R)6 (2.5%)
Asn (N)13 (5.3%)
Asp (D)18 (7.4%)
Cys (C)2 (0.8%)
Gln (Q)8 (3.3%)
Glu (E)16 (6.6%)
Gly (G)26 (10.7%)
His (H)9 (3.7%)
Ile (I)12 (4.9%)
Leu (L)22 (9.1%)
Lys (K)21 (8.6%)
Met (M)5 (2.1%)
Phe (F)11 (4.5%)
Pro (P)10 (4.1%)
Ser (S)8 (3.3%)
Thr (T)16 (6.6%)
Trp (W)1 (0.4%)
Tyr (Y)12 (4.9%)
Val (V)17 (7.0%)
Amino acid counting
Total number:243
Positively charged (Arg+Lys):27 (11.1%)
Negatively charged (Asp+Glu):34 (14.0%)
Aromatic (Phe+His+Try+Tyr):33 (13.6%)
Biochemical parameters
Atomic composition:C1218H1882N322O369S7
Molecular mass [Da]:27164.7
Theoretical pI:5.71
Extinction coefficient at 280 nm [M-1 cm-1]:23380 / 23505 (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 (0.80)good (0.76)good (0.63)good (0.70)excellent (0.81)good (0.72)
Alignments (obtained from PredictProtein.org)
SwissProt:P42212 (95% identity on 238 AAs), Q9U6Y3 (26% identity on 217 AAs)
TrEML:B6UPG7 (96% identity on 238 AAs), B7UCZ6 (96% identity on 238 AAs)
PDB:1myw (97% identity on 228 AAs), 1qxt (96% identity on 226 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:secreted (100%)
Bacteria:cytosol (50%)
Eukarya:cytosol (36%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:GO:0018298 (44%), GO:0008218 (31%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices: -
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[edit]
Categories
//cds/reporter/yfp
//function/reporter/fluorescence
Parameters
colorYellow