The Clustal Colour Scheme
This is the default Clustal colour scheme as used by ClustalX, Jalview and the Pfam-Squared Server. The actual colours are shown (which vary slightly in the different applications), followed by the rules as set out in the file colprot.par which comes with the clustalx application. This default colour file has a lot of redundancy, so only the rules that are needed are given below.
Rules are specified in this way:
(A,C,D): {50%, p,q,rstv}{85%, w,y}
The column residue is given first in the round brackets; more than one may be specified, in which case the rules apply to each of these residues. Next, the rule or rules are given in curly braces; only one rule has to be met for the colour to be applied. The minimum percentage is given first, followed by the residue or residues which must meet or exceed this percentage within the column. If a group of residues is concatenated together, such as 'rstv', then any combination of these residues in total must meet or exceed the given percentage for the colour to be applied. For residues or residue groups separated by commas, at least one of these must by itself exceed the percentage.
ClustalX
Jalview
Pfam2
Rules:
blue
blue
blue
(W,L,V,I,M,F): {50%, p}{60%, wlvimafcyhp}
(A): {50%, p}{60%, wlvimafcyhp}{85%, t,s,g}
(C): {50%, p}{60%, wlvimafcyhp}{85%, s}
red
red
red
(K,R): {60%, kr}{85%, q}
green
green
green
(T): {50%, ts}{60%, wlvimafcyhp}
(S): {50%, ts}{80%, wlvimafcyhp}
(N): {50%, n}{85%, d}
(Q): {50%, qe}{60%, kr}
pink
pink
pink
(C): {85%, c}
magenta
magenta
magenta
(D): {50%, de,n}
(E): {50%, de,qe}
orange
orange
orange
(G): {always}
cyan
cyan
cyan
(H,Y): {50%, p}{60%, wlvimafcyhp}
yellow
yellow
yellow
(P): {always}