6TLQ_1|Chain A|Nuclear receptor ROR-gamma|Homo sapiens (9606)
>3KWG_1|Chains A, B|Non-structural protein 1|Influenza A virus (381517)
>6BAQ_1|Chains A, B, C, D, E, F, G, H|BPI fold-containing family A member 1|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 \(c\).
\(|P_{f(6TLQ_1)}(2) \setminus P_{f(3KWG_1)}(2)|=108\),
\(|P_{f(3KWG_1)}(2) \setminus P_{f(6TLQ_1)}(2)|=55\).
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 1:10000000000111101001101001001100100000000010100110000011000010100000110110001001001100110110010111010000011110111101111010010010000111010011101101110001100110100010110100001110011111010011100000100100010111000100000001110111010100100001001011001011110111111000110
Pair
\(Z_2\)
Length of longest common subsequence
6TLQ_1,3KWG_1
163
6
6TLQ_1,6BAQ_1
177
4
3KWG_1,6BAQ_1
152
3
Newick tree
[
6TLQ_1:87.88,
[
3KWG_1:76,6BAQ_1:76
]:11.88
]
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 \((0.85)(0.8)(\frac{404
}{\log_{20}
404}-\frac{141}{\log_{20}141})=79.0\)
Status
Protein1
Protein2
d
d1/2
Query variables
6TLQ_1
3KWG_1
98
75.5
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]