1SHJ_1|Chains A, B|Caspase-7|Homo sapiens (9606)
>7JWD_1|Chains A, B|Retinol-binding protein 2|Homo sapiens (9606)
>2FVH_1|Chains A, B, C|Urease gamma subunit|Mycobacterium tuberculosis (1773)
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 \(c\).
\(|P_{f(1SHJ_1)}(2) \setminus P_{f(7JWD_1)}(2)|=129\),
\(|P_{f(7JWD_1)}(2) \setminus P_{f(1SHJ_1)}(2)|=54\).
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 1:0000011000001010011001110000100101111001000010111001001110111000000101001100100000001101101110010001101001101100101010110000110010111101001001001101001110000101000111010111100011100010011010111011001100010010110110010001100100000010100000110110110001010001000000
Pair
\(Z_2\)
Length of longest common subsequence
1SHJ_1,7JWD_1
183
3
1SHJ_1,2FVH_1
183
6
7JWD_1,2FVH_1
136
3
Newick tree
[
1SHJ_1:98.09,
[
7JWD_1:68,2FVH_1:68
]:30.09
]
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 \((0.85)(0.8)(\frac{400
}{\log_{20}
400}-\frac{138}{\log_{20}138})=78.9\)
Status
Protein1
Protein2
d
d1/2
Query variables
1SHJ_1
7JWD_1
102
76.5
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]