Part:BBa_K1159315

TMD of SERK Receptor from Physcomitrella patens with C-terminal GFP fusion in RFC[25]

This part codes for the Transmembrane Domain of SERK Receptor from Physcomitrella patens with a C-terminal (intracellular) GFPmut1 fusion; SERK TMD and GFPmut1 are seperated by a middle long linker. Still, a signal peptide is needed for membrane integration. 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
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI.rc site found at 863

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)
ATGGCCGGCCCTGGACAA ... CTCTACAAAACCGGT
ORF from nucleotide position -8 to 939 (excluding stop-codon)

Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)

1
101
201
301

MAGPGQPPFPPPPPFTPPPPQTPNGASGENSTGAIAGGVAAGAALLFAAPAIGFAWWRRRRPIEATGGGSGGGSGTGSKGEELFTGVVPILVELDGDVNG
HKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIE
LKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLSPDNHYLSTQSALSKDPNEKRDHMVLLEFV
TAAGITHGMDELYKTG*

Sequence features: (with their position in the amino acid sequence, see the list of supported features)

RFC25 scar (shown in bold):

66 to 67, 76 to 77

Amino acid composition:

Ala (A)	21 (6.6%)
Arg (R)	10 (3.2%)
Asn (N)	15 (4.7%)
Asp (D)	18 (5.7%)

Cys (C)	2 (0.6%)
Gln (Q)	10 (3.2%)
Glu (E)	18 (5.7%)
Gly (G)	40 (12.7%)

His (H)	10 (3.2%)
Ile (I)	15 (4.7%)
Leu (L)	21 (6.6%)
Lys (K)	20 (6.3%)

Met (M)	6 (1.9%)
Phe (F)	16 (5.1%)
Pro (P)	25 (7.9%)
Ser (S)	15 (4.7%)

Thr (T)	22 (7.0%)
Trp (W)	3 (0.9%)
Tyr (Y)	11 (3.5%)
Val (V)	18 (5.7%)

Amino acid counting

	Total number:	316
	Positively charged (Arg+Lys):	30 (9.5%)
	Negatively charged (Asp+Glu):	36 (11.4%)
	Aromatic (Phe+His+Try+Tyr):	40 (12.7%)

Biochemical parameters

	Atomic composition:	C₁₅₃₁H₂₃₄₂N₄₁₄O₄₆₂S₈
	Molecular mass [Da]:	34196.4
	Theoretical pI:	5.93
	Extinction coefficient at 280 nm [M^-1 cm^-1]:	32890 / 33015 (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 (0.73)	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 238 AAs), Q9U6Y3 (25% identity on 217 AAs)
	TrEML:	Q71RY9 (98% identity on 238 AAs), B6F2F5 (97% identity on 241 AAs)
	PDB:	1gfl (98% identity on 229 AAs), 2y0g (98% identity on 226 AAs)

Predictions (obtained from PredictProtein.org)

Subcellular Localization (reliability in brackets)

	Archaea:	secreted (100%)
	Bacteria:	secreted (74%)
	Eukarya:	cytosol (44%)

Gene Ontology (reliability in brackets)

	Molecular Function Ontology:	-
	Biological Process Ontology:	GO:0018298 (44%), GO:0008218 (31%)

Predicted features:

	Disulfid bridges:	-
	Transmembrane helices:	37 to 54 going inwards

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