1FXJ_1|Chains A, B|UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE|Escherichia coli (562)
>3SOM_1|Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P|Methylmalonic aciduria and homocystinuria type C protein|Homo sapiens (9606)
>3WOG_1|Chains A, B|Erythroagglutinin|Phaseolus vulgaris (3885)
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 \(c\).
\(|P_{f(1FXJ_1)}(2) \setminus P_{f(3SOM_1)}(2)|=82\),
\(|P_{f(3SOM_1)}(2) \setminus P_{f(1FXJ_1)}(2)|=84\).
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 1:1100110111111101001000110110011101110011011001111010110101101100110000101110100110101100111111000011110101111010010010010101111110101001010101000010101110000100000010010011111011010011101000010100010011111000100111101001001011000101001001000001001111111100110101010100100101000111010101100101101011000111000010100110010111100111110
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 \((0.85)(0.8)(\frac{617
}{\log_{20}
617}-\frac{286}{\log_{20}286})=92.6\)
Status
Protein1
Protein2
d
d1/2
Query variables
1FXJ_1
3SOM_1
115
109
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]