Coding

Part:BBa_K1159019

Designed by: TU Munich 2013   Group: iGEM13_TU-Munich   (2013-05-17)
Revision as of 15:04, 8 October 2013 by JohannaB (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

Membrane-anchored Human Protein Phosphatase 1 (PP1) in RFC[25] N-Part

This part codes for a membrane-anchored version of the Human Protein Phosphatase 1 (PP1) for the chassis Physcomitrella patens. Please see subparts for for further description. This construct is flanked by RFC[25] N-part prefix and suffix. Note: This means only protein fusions to the C-terminus of this part is possible, adding promoters (typically RFC[10]) into the prefix or terminators/IRES (typically RFC[10]) into the suffix of this part is nevertheless possible.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 643
    Illegal BamHI site found at 107
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 1092
    Illegal BsaI.rc site found at 1030
    Illegal BsaI.rc site found at 2010

Protein data table for BioBrick BBa_ automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25 N-Part using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)
 AACAATGCCTGGT ... CTCTACAAAACCGGT
 ORF from nucleotide position 5 to 2086 (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 
601 		MPGEVAWWRPLFLIALMPIGVLSNAEGDALNTTGGSADLDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDI
HGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIV
DEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVT
LFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKKTGSAWSHPQFEKGENLYFQSGTGPGQPPFPPPPPFTPPPPQT
PNGASGENSTGAIAGGVAAGAALLFAAPAIGFAWWRRRRPIEATGGGSGGGSGTGSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKF
ICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYN
SHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLSPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
RFC25 scar (shown in bold): 33 to 34, 359 to 360, 380 to 381, 444 to 445, 454 to 455
Strep-tag II: 363 to 370
TEV cleavage site: 372 to 378
Amino acid composition:
Ala (A)41 (5.9%)
Arg (R)29 (4.2%)
Asn (N)31 (4.5%)
Asp (D)42 (6.1%)
Cys (C)15 (2.2%)
Gln (Q)25 (3.6%)
Glu (E)43 (6.2%)
Gly (G)70 (10.1%)
His (H)17 (2.4%)
Ile (I)38 (5.5%)
Leu (L)66 (9.5%)
Lys (K)44 (6.3%)
Met (M)13 (1.9%)
Phe (F)37 (5.3%)
Pro (P)46 (6.6%)
Ser (S)34 (4.9%)
Thr (T)36 (5.2%)
Trp (W)9 (1.3%)
Tyr (Y)24 (3.5%)
Val (V)34 (4.9%)
Amino acid counting
Total number:694
Positively charged (Arg+Lys):73 (10.5%)
Negatively charged (Asp+Glu):85 (12.2%)
Aromatic (Phe+His+Try+Tyr):87 (12.5%)
Biochemical parameters
Atomic composition:C3463H5334N924O1015S28
Molecular mass [Da]:77049.7
Theoretical pI:5.85
Extinction coefficient at 280 nm [M-1 cm-1]:85260 / 86198 (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 (0.71)good (0.75)good (0.72)excellent (0.81)excellent (0.80)good (0.71)
Alignments (obtained from PredictProtein.org)
SwissProt:P36873 (100% identity on 322 AAs), P36874 (99% identity on 322 AAs), P61287 (99% identity on 322 AAs), P63087 (99% identity on 322 AAs), P63088 (99% identity on 322 AAs), Q6NVU2 (99% identity on 322 AAs), Q7SZ10 (99% identity on 322 AAs), P42212 (98% identity on 238 AAs), Q8MJ46 (98% identity on 322 AAs)
TrEML:F6YKN7 (100% identity on 322 AAs), F7AYW3 (100% identity on 305 AAs), F7GFU1 (100% identity on 322 AAs), G5AWL7 (100% identity on 296 AAs), H9FWE1 (100% identity on 321 AAs), K7A7K5 (100% identity on 322 AAs), Q4R4V0 (100% identity on 322 AAs), Q9UPN1 (100% identity on 293 AAs), B5KFI8 (99% identity on 322 AAs), F8VYE8 (99% identity on 294 AAs)
PDB:1it6 (100% identity on 293 AAs), 1jk7 (100% identity on 294 AAs), 2bcd (100% identity on 293 AAs), 2bdx (100% identity on 293 AAs), 2o8a (100% identity on 295 AAs), 2o8g (100% identity on 295 AAs), 1u32 (98% identity on 293 AAs)
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (100%)
Bacteria:cytosol (59%)
Eukarya:cytosol (40%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology:GO:0005515 (70%), GO:0004722 (70%)
Biological Process Ontology:GO:0051301 (28%), GO:0005977 (27%)
 
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