4KBR_1|Chains A, B, C, D, E, F, G, H|Glycolipid transfer protein domain-containing protein 1|Mus musculus (10090)
>1JHI_1|Chains A, B|5'-D(*AP*CP*CP*(HEH)GP*GP*T)-3'|
>6IKN_1|Chains A, B, C, D|Growth arrest-specific protein 7|Mus musculus (10090)
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 \(c\).
\(|P_{f(4KBR_1)}(2) \setminus P_{f(1JHI_1)}(2)|=147\),
\(|P_{f(1JHI_1)}(2) \setminus P_{f(4KBR_1)}(2)|=5\).
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 1:0100000010101111010001000101110001111011101100111110110001110101100100010000000100111001000110100000100100100011010011011011101100000010000100010010110000111001101110111000111011010000011011101111100100100010100011011
Pair
\(Z_2\)
Length of longest common subsequence
4KBR_1,1JHI_1
152
1
4KBR_1,6IKN_1
178
4
1JHI_1,6IKN_1
192
2
Newick tree
[
6IKN_1:97.46,
[
4KBR_1:76,1JHI_1:76
]:21.46
]
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 \((0.85)(0.8)(\frac{223
}{\log_{20}
223}-\frac{6}{\log_{20}6})=77.1\)
Status
Protein1
Protein2
d
d1/2
Query variables
4KBR_1
1JHI_1
100
51.5
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]