polypeptides. The preci method of calculation gets a bit abstru, but an illustration may demystify some aspects.
The procedure for calculating a BLOSUM matrix is bad on a likelihood method estimating the occurrence of each possible pairwi substitution. A very simple illustration of such a calculation for a
tnkvery short gment is given below to illustrate the process. The polypeptides were initially aligned using an identity scoring matrix. Only aligned blocks are ud to calculate the BLOSUMs.
Assume that the following 5 proteins were aligned as follows:
AVAAA
AVAAA
翻译孙宁AVAAA
AVLAAdanni
VVAAL
First, we have to decide whether each quence should count equally in this process. If this databa were a global reprentation, they should. However, databas of today typically over-reprent certain class of proteins. Therefore, the first step is to reduce this over-reprentation and make the datat more reprentative. One method of doing this is to count all the identical blocks as if they were a single block, reducing the aligned databa to:
AVAAA
AVLAAalexander graham bell
VVAAL
Next, at each position, we must calculate the obrved and expected pairwi substitutions. At position 1, we have:chess是什么意思
Apropertyname
A A-A, A-V, A-V are the obrved substitutions. Without specifying the necessary calculations, one V can e that the substitution of A for A or A for V are quite likely and that A-X is not!
Why is BLOSUM62 called BLOSUM62? Basically, this is becau all blocks who members shared at least 62% identity with ANY other member of that block were averaged and reprented as 1 quence. How would this work with our example?
AVAAA
AVAAA
AVAAA
AVLAA
VVAAL分词的用法
9695
1-4 are all 80% identical to each other. Sequence 5 is less than 62% (it is 60% identical to 1-3 and t0 #4). This means that the BLOCK ud to make a BLOSUM62 would be: (note the averaging!)
AVA(3/4)AA
L(1/4)
VVA*****AL
How does the matrix relate to structural similarity? Most biochemists group the amino acids as follows: G,A,V,L,I, M aliphatic (though some would not include G)
S,T,C hydroxyl, sulfhydryl, polar
otdrN,Q amide side chainsbl是什么意思
F,W,Y aromatic
H,K,R basic
D,E acidic
Some rather anomalous substitutions relative to the groupings are highlighted below. For example, it ems VERY surprising to me that K-E substitution is not unusual. That changes charge! This suggests that what evolution thinks is “similar” is not necessarily similar to the molecular biologist.
(Of cou r, it is also possible that K-E substitu tion in one position is also often correlated with a E-K substitution elwhere, and that what one retains is the electrostatic interaction between charged residues. Much like G-C or C-G compensating mu tations in stem-
