3IQE_1|Chains A, B, C, D, E, F|F420-dependent methylenetetrahydromethanopterin dehydrogenase|Methanopyrus kandleri (2320)
>3PGD_1|Chains A, D|HLA class II histocompatibility antigen, DR alpha chain|Homo sapiens (9606)
>1RYK_1|Chain A|Protein yjbJ|Escherichia coli (562)
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 \(c\).
\(|P_{f(3IQE_1)}(2) \setminus P_{f(3PGD_1)}(2)|=84\),
\(|P_{f(3PGD_1)}(2) \setminus P_{f(3IQE_1)}(2)|=64\).
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 1:1011011110010110011101110001000010101110010101001011101110110010101110111011111100100111000011111101111010001000111011101011111000110110111001011011110111011001100110010000100001101110000110000100101110111110110011010101011000000011111010011001101100100100000111001011010110000110010
Pair
\(Z_2\)
Length of longest common subsequence
3IQE_1,3PGD_1
148
3
3IQE_1,1RYK_1
167
3
3PGD_1,1RYK_1
165
3
Newick tree
[
1RYK_1:85.79,
[
3IQE_1:74,3PGD_1:74
]:11.79
]
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 \((0.85)(0.8)(\frac{476
}{\log_{20}
476}-\frac{193}{\log_{20}193})=82.5\)
Status
Protein1
Protein2
d
d1/2
Query variables
3IQE_1
3PGD_1
102
86
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]