Clustal X Colour Scheme

This is an emulation of the default colourscheme used for alignments in Clustal X, a graphical interface for the ClustalW multiple sequence alignment program. Each residue in the alignment is assigned a colour if the amino acid profile of the alignment at that position meets some minimum criteria specific for the residue type.

The table below gives these criteria as clauses: {>X%,xx,y}, where X is the threshold percentage presence for any of the xx (or y) residue types.
For example, K or R is coloured red if the column includes more than 60% K or R (combined), or more than 80% of either K or R or Q (individually).

Clustal X Default Colouring
Category | Colour | Residue at position | { Threshold, Residue group }
--- | --- | --- | ---
Hydrophobic | BLUE | A,I,L,M,F,W,V | {>60%, WLVIMAFCHP}
C | {>60%, WLVIMAFCHP}
Positive charge | RED | K,R | {>60%,KR},{>80%, K,R,Q}
Negative charge | MAGENTA | E | {>60%,KR},{>50%,QE},{>85%,E,Q,D}
D | {>60%,KR}, {>85%, K,R,Q}, {>50%,ED}
Polar | GREEN | N | {>50%, N}, {>85%, N,Y}
Q | {>60%,KR},{>50%,QE},{>85%,Q,E,K,R}
S,T | {>60%, WLVIMAFCHP}, {>50%, TS}, {>85%,S,T}
Cysteines | PINK | C | {>85%, C}
Glycines | ORANGE | G | {>0%, G}
Prolines | YELLOW | P | {>0%, P}
Aromatic | CYAN | H,Y | {>60%, WLVIMAFCHP}, {>85%, W,Y,A,C,P,Q,F,H,I,L,M,V}
Unconserved | WHITE | any / gap | If none of the above criteria are met