1CZG_1|Chains A, B, C, D, E|SHIGA TOXIN B-CHAIN|Phage h30 (12371)
>9NIH_1|Chain A|HLA class II histocompatibility antigen, DR alpha chain|Homo sapiens (9606)
>9BCC_1|Chains A, B|Kelch domain-containing protein 2|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 \(c\).
\(|P_{f(1CZG_1)}(2) \setminus P_{f(9NIH_1)}(2)|=27\),
\(|P_{f(9NIH_1)}(2) \setminus P_{f(1CZG_1)}(2)|=111\).
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 1:010010101000000000010101100011000101001110101011010100010001101001110
Pair
\(Z_2\)
Length of longest common subsequence
1CZG_1,9NIH_1
138
3
1CZG_1,9BCC_1
211
3
9NIH_1,9BCC_1
181
4
Newick tree
[
9BCC_1:10.27,
[
1CZG_1:69,9NIH_1:69
]:37.27
]
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 \((0.85)(0.8)(\frac{258
}{\log_{20}
258}-\frac{69}{\log_{20}69})=61.4\)
Status
Protein1
Protein2
d
d1/2
Query variables
1CZG_1
9NIH_1
78
52
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]