4QJB_1|Chains A, B|Haloacid dehalogenase-like hydrolase|Plasmodium falciparum (36329)
>6HOW_1|Chains A, B, C|Pteridine reductase|Trypanosoma brucei brucei (5702)
>8IUI_1|Chains A, B|Fibroinase|Bombyx mori (7091)
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 \(c\).
\(|P_{f(4QJB_1)}(2) \setminus P_{f(6HOW_1)}(2)|=80\),
\(|P_{f(6HOW_1)}(2) \setminus P_{f(4QJB_1)}(2)|=75\).
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 1:11000000100110001001000010001011100101011000001000010011010001101111010011010011100100001011111010101010001001100110001010100100010100011110100000101000100010101101011000110110100111011001100010100001000101100100010110000001011001000001010011111010001011011000111001000100011011100000110011001001
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 \((0.85)(0.8)(\frac{584
}{\log_{20}
584}-\frac{288}{\log_{20}288})=83.1\)
Status
Protein1
Protein2
d
d1/2
Query variables
4QJB_1
6HOW_1
104
102.5
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]