User GuidesSnapGene FAQ Alignment and AssemblyWhat are the SnapGene Protein Alignment Color Highlighting Schemes?

What are the SnapGene Protein Alignment Color Highlighting Schemes?

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