Coding

Part:BBa_K1159104

Designed by: Dong-Jiunn Jeffery TRUONG   Group: iGEM13_TU-Munich   (2013-09-14)

N-terminal Phytochrome Interacting Factor 6 (PIF6) in RFC[25]

N-terminal Phytochrome Interacting Factor 6 (PIF6) is known to be recognized by Phytochrome B (PhyB) under red light exposition. This interaction between PhyB and PIF6 can be reverted by irradiation with far-red light. This part contains only the first 100 amino acid residues of PIF6 which is sufficient for light-dependent binding to PhyB. N- and C-terminal protein fusions seems not to affect the binding of PhyB. This part 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)
 ATGGCCGGCATGTTCTTA ... CATGTTGACACCGGT
 ORF from nucleotide position -8 to 303 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 		MAGMFLPTDYCCRLSDQEYMELVFENGQILAKGQRSNVSLHNQRTKSIMDLYEAEYNEDFMKSIIHGGGGAITNLGDTQVVPQSHVAAAHETNMLESNKH
VDTG*
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)7 (6.7%)
Arg (R)3 (2.9%)
Asn (N)7 (6.7%)
Asp (D)6 (5.8%)
Cys (C)2 (1.9%)
Gln (Q)6 (5.8%)
Glu (E)8 (7.7%)
Gly (G)9 (8.7%)
His (H)5 (4.8%)
Ile (I)5 (4.8%)
Leu (L)8 (7.7%)
Lys (K)4 (3.8%)
Met (M)6 (5.8%)
Phe (F)3 (2.9%)
Pro (P)2 (1.9%)
Ser (S)7 (6.7%)
Thr (T)6 (5.8%)
Trp (W)0 (0.0%)
Tyr (Y)4 (3.8%)
Val (V)6 (5.8%)
Amino acid counting
Total number:104
Positively charged (Arg+Lys):7 (6.7%)
Negatively charged (Asp+Glu):14 (13.5%)
Aromatic (Phe+His+Try+Tyr):12 (11.5%)
Biochemical parameters
Atomic composition:C495H774N140O163S8
Molecular mass [Da]:11550.9
Theoretical pI:4.98
Extinction coefficient at 280 nm [M-1 cm-1]:5960 / 6085 (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 (0.76)good (0.76)good (0.71)good (0.78)excellent (0.81)good (0.70)
Alignments (obtained from PredictProtein.org)
SwissProt:Q8L5W7 (100% identity on 99 AAs), Q8L5W8 (51% identity on 73 AAs)
TrEML:D0EDQ7 (100% identity on 83 AAs), F4IX36 (100% identity on 83 AAs), C0SVF8 (98% identity on 90 AAs)
PDB: -
Predictions (obtained from PredictProtein.org)
Subcellular Localization (reliability in brackets)
Archaea:cytosol (100%)
Bacteria:secreted (78%)
Eukarya:secreted (14%)
Gene Ontology (reliability in brackets)
Molecular Function Ontology:GO:0005515 (70%)
Biological Process Ontology:GO:0006350 (43%), GO:0010017 (43%)
 
Predicted features:
Disulfid bridges:11 to 12
Transmembrane helices: -
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Categories
Parameters
None