How to interpret Percent identity matrix created by Clustal Omega?

Question

I did a multiple sequence alignment using Clustal omega. checked similarity for 3 protein sequences : aspartyl aminopeptidase [Homo sapiens], aminopeptidase P (APP) [Plasmodium falciparum 3D7], yeast aminopeptidase (S000001586)APE1. I got Percent identity matrix as

Percent Identity Matrix - created by Clustal2.1

 1: PF3D7_1454400              100.00   16.18   20.35
 2: gi|5902181|gb|AAD01211.2|   16.18  100.00   29.66
 3: S000001586                  20.35   29.66  100.00 

My doubts:

1. I would like to know how to interpret this matrix result
2. Coming back to sequence alignments results, when I click on 'Show colors', the alignment summary is colored in 4 colors - red, green, blue and pink. Can anyone help me in decoding the color reference of alignment summary?

Thanks

Answer 1

        Gene-1   Gene-2    Gene-3
Gene-1  100.00    16.18     20.35
Gene-2  16.18    100.00     29.66
Gene-3  20.35     29.66    100.00 

Gene-1 and Gene-1 have 100% similarity (and all the other diagonal elements). Gene-1 and Gene-2 have 16.15% similarity, and so on. Therefore the matrix is symmetric M(i,j) = M(j,i).

You can also show just the upper triangular part of this matrix and that would be sufficient.

        Gene-1   Gene-2    Gene-3
Gene-1  100.00    16.18     20.35
Gene-2           100.00     29.66
Gene-3                     100.00

The colours basically denote the type (molecular nature) of residue. Have a look at this and this.