Coding

Part:BBa_K1159316

Designed by: TU Munich 2013   Group: iGEM13_TU-Munich   (2013-09-16)

SERK-Receptor TMD with C-terminal GFP and N-terminal Strep-tag II TEV-site linker in RFC[25]

This part codes for the Transmembrane Domain of SERK Receptor from Physcomitrella patens with a C-terminal (intracellular) GFPmut1 fusion and a N-terminal fusion to a linker containing Strep-tag II and a TEV cleavage site; SERK TMD and GFPmut1 are seperated by a middle long linker. This part is flanked by RFC[25] pre- and suffix for further protein fusions.

Note: A signal peptide is needed for membrane integration.

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
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 8
    Illegal BsaI.rc site found at 926

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)
 ATGGCCGGCAGCGCTTGG ... CTCTACAAAACCGGT
 ORF from nucleotide position -8 to 1002 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

101 
201 
301 
MAGSAWSHPQFEKGENLYFQSGTGPGQPPFPPPPPFTPPPPQTPNGASGENSTGAIAGGVAAGAALLFAAPAIGFAWWRRRRPIEATGGGSGGGSGTGSK
GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLSPDNHYLST
QSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
Strep-tag II: 6 to 13
TEV cleavage site: 15 to 21
RFC25 scar (shown in bold): 23 to 24, 87 to 88, 97 to 98
Amino acid composition:
Ala (A)22 (6.5%)
Arg (R)10 (3.0%)
Asn (N)16 (4.7%)
Asp (D)18 (5.3%)
Cys (C)2 (0.6%)
Gln (Q)12 (3.6%)
Glu (E)20 (5.9%)
Gly (G)43 (12.8%)
His (H)11 (3.3%)
Ile (I)15 (4.5%)
Leu (L)22 (6.5%)
Lys (K)21 (6.2%)
Met (M)6 (1.8%)
Phe (F)18 (5.3%)
Pro (P)26 (7.7%)
Ser (S)18 (5.3%)
Thr (T)23 (6.8%)
Trp (W)4 (1.2%)
Tyr (Y)12 (3.6%)
Val (V)18 (5.3%)
Amino acid counting
Total number:337
Positively charged (Arg+Lys):31 (9.2%)
Negatively charged (Asp+Glu):38 (11.3%)
Aromatic (Phe+His+Try+Tyr):45 (13.4%)
Biochemical parameters
Atomic composition:C1638H2488N442O495S8
Molecular mass [Da]:36548.9
Theoretical pI:5.88
Extinction coefficient at 280 nm [M-1 cm-1]:39880 / 40005 (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 (0.73)good (0.75)good (0.76)excellent (0.84)excellent (0.81)good (0.71)
Alignments (obtained from PredictProtein.org)
SwissProt:P42212 (98% identity on 237 AAs), Q9U6Y3 (25% identity on 217 AAs)
TrEML:B6UPG7 (98% identity on 237 AAs), Q71RY9 (98% identity on 237 AAs), Q8GHE2 (98% identity on 237 AAs)
PDB:1emm (97% identity on 221 AAs), 1gfl (97% identity on 230 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:secreted (100%)
Bacteria:secreted (77%)
Eukarya:cytosol (47%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology: -
Biological Process Ontology:GO:0018298 (44%), GO:0008218 (31%)
 
Predicted features:
Disulfid bridges: -
Transmembrane helices:57 to 74 going inwards
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
//chassis/eukaryote/ppatens
Parameters
None