What are the SnapGene Protein Alignment Color Highlighting Schemes?

November 02, 2022 04:03

SnapGene allows amino acid color highlighting based on three color schemes as detailed below.

Physicochemical Properties (Zappo)

Residues are coloured according to their physicochemical properties as follows:

Category	Colour	Residues
Aliphatic/hydrophobic		I, L, V, A, M
Aromatic		F, W, Y
Positive		K, R, H
Negative		D, E
Hydrophilic		S, T, N, Q
Conformationally special		P, G
Cysteine		C

Properties + Conservation (Clustal X)

Residues are colored according to their properties and conservation using the default Clustal X coloring scheme, as follows:

Category	Colour	Residue
Hydrophobic		A, I, L, M, F, W, V, C
Positive charge		K, R
Negative charge		E, D
Polar		N, Q, S, T
Glycines		G
Prolines		P
Aromatic		H,Y
Unconserved	WHITE	any / gap

Transmembrane Tendency (Zhao and London)

Residues are coloured according to their "transmembrane tendency", as defined by Zhao and London, 2006:

Residue	Colour
Lys (K)		Most Hydrophilic
Asp (D)
Glu (E)
Arg (R)
Gln (Q)
Asn (N)
Pro (P)
His (H)
Ser (S)
Thr (T)
Cys (C)
Gly (G)		Neutral
Ala (A)
Tyr (Y)
Met (M)
Val (V)
Trp (W)
Leu (L)
Ile (I)
Phe (F)		Least Hydrophilic