VNRLQQNIVSL____________EVDHKVANYKPQVEPFGHGPIFMATALVPGLYLLPL VNRLQQSIVSLRDAFNDGTKLLEELDHRVLNYKPQANPFGNGPIFMVTAIVPGLHLLPIThe gaps arise from

- a)
- that the two sequences arose
independently of each other (implying that the alignment is entirely arbitrary,
with amino acid
*i*in one protein being aligned to amino acid*j*in the other is occurring no more frequently than expected by chance, which is equal to the product of the individual frequencies with which amino acids*i*and*j*occur in the database)

(1)

- b)
- that the two sequences have evolved
from some common ancestral sequence
after
*t*units of evolution where*t*is measured in PAM units [Gonnet, 1994b].

(2) |

where

(3) |

The entries of the Dayhoff matrix are the logarithm of the quotient of these two probabilities. Note that scores represent the probabilities that the two sequences have a common ancestor. The larger the score is the more likely it is that the two sequences are homologous and therefore have a common ancestor.