What does the PAM value mean?

• Multiple substitutions of amino acids lead to underestimation of evolutionary distances between two homologous proteins and as a consequence the observed percentage of difference or distance between two protein sequences is not proportional to the actual evolutionary difference.
• The PAM value corrects for this underestimation of distance and is proportional to the true evolutionary distance between two proteins. PAM (Dayhoff and Eck, 1968) is the number of Accepted Point Mutations per 100 amino acids.

Some PAM values and their corresponding observed distances

PAM Value	Distance(%)
80	50
100	60
200	75
250	85	<- Twilight zone
300	92

(From Doolittle, 1987, Of URFs and ORFs, University Science Books)

When the PAM distance value between two distantly related proteins nears the value 250 it becomes difficult to tell whether the two proteins are homologous, or that they are two at randomly taken proteins that can be aligned by chance. In that case we speak of the 'twilight zone'.

The relation between the observed percentage in distance of two sequences versus PAM value. Two randomly diverging sequences change in a negatively exponential fashion. After the insertion of gaps to two random sequences, it can be expected that they will be 80 - 90 % dissimilar (from Doolittle, 1987 ).

"

The relation between the observed percentage in distance of two sequences versus PAM value. Two randomly diverging sequences change in a negatively exponential fashion. After the insertion of gaps to two random sequences, it can be expected that they will be 80 - 90 % dissimilar (from Doolittle, 1987 )

Proteins evolve at highly different rates

	Rate of Change (PAMs / 100 myrs)	Theoretical Lookback Time (myrs)
Pseudogenes	400	45
Fibrinopeptides	90	200
Lactalbumins	27	670
Lysozymes	24	850
Ribonucleases	21	850
Haemoglobins	12	1500
Acid proteases	8	2300
Cytochrome c	4	5000
Glyceraldehyde-P dehydrogenase	2	9000
Glutamate dehydrogenase	1	18000

PAM = number of Accepted Point Mutations per 100 amino acids. Useful lookback time = 360 PAMs

Some Important Dates in History

Origin of the Universe	15 billion yrs
Formation of the Solar System	4.6 "
First Self-replicating System	3.5 "
Prokaryotic-Eukaryotic Divergence	2.0 "
Plant-Animal Divergence	1.0 "
Invertebrate-Vertebrate Divergence	0.5 "
Mammalian Radiation Beginning	0.1 "

From: Doolittle, Of URFs and ORFs, 1987

---

Last updated: 22 September 1997.

---