9HKE_1|Chain A|Flavin-dependent monooxygenase|Escherichia coli (562)
>6XHH_1|Chains A, B|JSC1_58120g3|[Leptolyngbya] sp. JSC-1 (1487953)
>2PKD_1|Chains A, B, C, D, E, F|SLAM family member 5|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 \(c\).
\(|P_{f(9HKE_1)}(2) \setminus P_{f(6XHH_1)}(2)|=125\),
\(|P_{f(6XHH_1)}(2) \setminus P_{f(9HKE_1)}(2)|=43\).
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 1:01100001111111111101101100011010100000000101111010100101001100111100000111111101100010110000101000100101000010111100100001110001111011000101010001000101111101110010011000010001010101010010100111101001001111001011110100011101110100100100000101000001101110010010000001101000111110011111001000011110111011011111110110011101111000100101001001100000011101001000000001011010101
Pair
\(Z_2\)
Length of longest common subsequence
9HKE_1,6XHH_1
168
4
9HKE_1,2PKD_1
180
4
6XHH_1,2PKD_1
146
3
Newick tree
[
9HKE_1:91.25,
[
6XHH_1:73,2PKD_1:73
]:18.25
]
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 \((0.85)(0.8)(\frac{553
}{\log_{20}
553}-\frac{182}{\log_{20}182})=107.\)
Status
Protein1
Protein2
d
d1/2
Query variables
9HKE_1
6XHH_1
134
99
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]