SEC65/YML105C Additional Physico-chemical Properties Help

Physico-chemical properties were determined using the ProtParam tool available through ExPASy to analyze the primary protein sequence for atomic composition, extinction coefficient, estimated half-life, instability index and aliphatic index. Transcript translation calculations were determined using CodonW.


A.A. Composition
Ala[A] 13 4.8%
Arg[R] 17 6.2%
Asn[N] 18 6.6%
Asp[D] 14 5.1%
Cys[C] 3 1.1%
Gln[Q] 7 2.6%
Glu[E] 25 9.2%
Gly[G] 15 5.5%
His[H] 5 1.8%
Ile[I] 17 6.2%
Leu[L] 19 7.0%
Lys[K] 29 10.6%
Met[M] 8 2.9%
Phe[F] 14 5.1%
Pro[P] 23 8.4%
Ser[S] 14 5.1%
Thr[T] 11 4.0%
Trp[W] 0 0.0%
Tyr[Y] 6 2.2%
Val[V] 15 5.5%
Total Length 273

Instability index
Instability index (II) 43.74
This classifies the protein as unstable

Atomic composition
Carbon 1384
Hydrogen 2214
Nitrogen 388
Oxygen 408
Sulfur 11
Total number of atoms 4405
Formula = C1384H2214N388O408S11

Estimated half-life
Escherichia coli (in vivo) >10 hours
mammalian reticulocytes (in vitro) 30 hours
yeast (in vivo) >20 hours

Extinction Coefficients at 280 nm
assuming ALL Cys residues appear as half cystines 9065 M-1 cm-1
assuming NO Cys residues appear as half cystines 8940 M-1 cm-1
assuming all Cys residues are reduced 8940 M-1 cm-1
assuming all pairs of Cys residues form cystines 9065 M-1 cm-1

Aliphatic index
Aliphatic index 72.12

Coding Region Translation Calculations
Codon Bias 0.158
Codon Adaptation Index 0.173
Frequency of Optimal Codons 0.502
Hydropathicity of Protein -0.740
Aromaticity Score 0.073