3PNS_1|Chains A, B, C, D, E, F, G, H, I, J, K, L|Uridine phosphorylase|Vibrio cholerae O1 biovar El Tor (243277)
>3RUA_1|Chains A, B, C, D|WbgU|Plesiomonas shigelloides (703)
>1XOP_1|Chain A|Hemagglutinin|null
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 \(c\).
\(|P_{f(3PNS_1)}(2) \setminus P_{f(3RUA_1)}(2)|=66\),
\(|P_{f(3RUA_1)}(2) \setminus P_{f(3PNS_1)}(2)|=102\).
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 1:001100111000110111001010110111111011010011011001111100000010010101001110001111100011100110111001101100111010101101110010101011010111101111101011011011100011010111010000101100000010101100101010010011110101001011010100110110111111000000110010100001001011101100110
Pair
\(Z_2\)
Length of longest common subsequence
3PNS_1,3RUA_1
168
3
3PNS_1,1XOP_1
171
3
3RUA_1,1XOP_1
197
4
Newick tree
[
1XOP_1:94.81,
[
3PNS_1:84,3RUA_1:84
]:10.81
]
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 \((0.85)(0.8)(\frac{612
}{\log_{20}
612}-\frac{261}{\log_{20}261})=98.7\)
Status
Protein1
Protein2
d
d1/2
Query variables
3PNS_1
3RUA_1
127
109.5
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]