8DML_1|Chains A, C, E, G|VtrA|Vibrio parahaemolyticus (670)
>8YFU_1|Chains A, B|Solute carrier family 53 member 1|Homo sapiens (9606)
>6BAZ_1|Chains A, B, C, D|L-lactate dehydrogenase A chain|Homo sapiens (9606)
Let \(P_w(n)\) be the set of distinct subwords (intervals) in a word \(w\).
Let \(p_w(n)\) be the cardinality of \(P_w(n)\).
Let \(f(c)\) be the sequence in FASTA with 4-symbol Protein Data Bank code \(c\).
\(|P_{f(8DML_1)}(2) \setminus P_{f(8YFU_1)}(2)|=11\),
\(|P_{f(8YFU_1)}(2) \setminus P_{f(8DML_1)}(2)|=207\).
Let
\(
Z_k(x,y)=|P_x(k)\setminus P_y(k)|+|P_y(k)\setminus P_x(k)|
\)
be a LZ76 style (set of subwords) Jaccard distance numerator for \(P(k)\).Hydrophobic-polar version of Sequence 1:1010000101010000101100010100011111101101001110010111000010101100000000011000001000010001100100
Pair
\(Z_2\)
Length of longest common subsequence
8DML_1,8YFU_1
218
3
8DML_1,6BAZ_1
180
4
8YFU_1,6BAZ_1
170
3
Newick tree
[
8DML_1:10.46,
[
6BAZ_1:85,8YFU_1:85
]:19.46
]
Let d be the
Otu--Sayood
distance d.
Let d1 be the Otu--Sayood distance d1. (This makes the 4TYN sequence AAAAAA a close match...)
A roughly speaking expected distance is \((0.85)(0.8)(\frac{694
}{\log_{20}
694}-\frac{94}{\log_{20}94})=173.\)
Status
Protein1
Protein2
d
d1/2
Query variables
8DML_1
8YFU_1
222
127
Was not able to put for d Was not able to put for d1
In notation analogous to
[Theorem 16, Kjos-Hanssen, Niraula and Yoon (2022)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]