5PZM_1|Chains A, B|RNA-directed RNA polymerase|Hepatitis C virus genotype 1b (isolate Con1) (333284)
>5RZT_1|Chain A|Isoform 2 of Band 4.1-like protein 3|Homo sapiens (9606)
>2VAT_1|Chains A, B, C, D, E, F, G, H, I, J, K, L|ACETYL-COA--DEACETYLCEPHALOSPORIN C ACETYLTRANSFERASE|ACREMONIUM CHRYSOGENUM (5044)
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 \(c\).
\(|P_{f(5PZM_1)}(2) \setminus P_{f(5RZT_1)}(2)|=132\),
\(|P_{f(5RZT_1)}(2) \setminus P_{f(5PZM_1)}(2)|=44\).
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 1:1010001011110101100001110110001100001101000001010000101001011000000110010101001010110100100101100100011011001001000110010011001100000110001110001101010011001101111101110100011100110011011110001100011001011101101000111110000010001000010100010000011101001100100010111110000100010000010111000010010001011110011010000111010011110001100000101011001100001111011010001011000000101100101001001000100111011100100011001110111011011101111001101111000100110001011000101101101100101101101000011010011001001111110110001001010110011011001001101110001010111110010100111110011010001001010111
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 \((0.85)(0.8)(\frac{860
}{\log_{20}
860}-\frac{286}{\log_{20}286})=156.\)
Status
Protein1
Protein2
d
d1/2
Query variables
5PZM_1
5RZT_1
200
149
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]