4FCO_1|Chain A|Beta-secretase 1|Homo sapiens (9606)
>2UYI_1|Chains A, B|KINESIN-LIKE PROTEIN KIF11|HOMO SAPIENS (9606)
>6QVD_1|Chains A, B|Chloride channel protein 1|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 \(c\).
\(|P_{f(4FCO_1)}(2) \setminus P_{f(2UYI_1)}(2)|=87\),
\(|P_{f(2UYI_1)}(2) \setminus P_{f(4FCO_1)}(2)|=59\).
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 1:1100000000011001010101100000010011001011011001010010100101011011001011100100011111110111000000010000001001101100011111011001101101101010101111000001110100101111110101101000101110011000011011010101111110000111011101111110001001011001100010001111010101001010000000000110010001011001101110010110000011011111001101011001101111101011101000010101110001011001100000000111000001011111110110111001000111110100100010011101111010100010011000000
Pair
\(Z_2\)
Length of longest common subsequence
4FCO_1,2UYI_1
146
3
4FCO_1,6QVD_1
148
5
2UYI_1,6QVD_1
168
4
Newick tree
[
6QVD_1:81.10,
[
4FCO_1:73,2UYI_1:73
]:8.10
]
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 \((0.85)(0.8)(\frac{801
}{\log_{20}
801}-\frac{368}{\log_{20}368})=117.\)
Status
Protein1
Protein2
d
d1/2
Query variables
4FCO_1
2UYI_1
148
137
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]