6UGU_1|Chains A, C[auth H]|PF06438179 Fab Heavy Chain|Homo sapiens (9606)
>8YEF_1|Chain A|Heavy chain of F5-77|Homo sapiens (9606)
>8PKY_1|Chains A, B|histidine kinase|Chloroflexus aggregans (152260)
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 \(c\).
\(|P_{f(6UGU_1)}(2) \setminus P_{f(8YEF_1)}(2)|=89\),
\(|P_{f(8YEF_1)}(2) \setminus P_{f(6UGU_1)}(2)|=35\).
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 1:0101000111110111010100110111100011011000100110111010000100100010010101010000000110101001000001100000000100000110100101001000110111111000000110111101100011011010100111001100111110001100100110110001100001001000100001000101000000
Pair
\(Z_2\)
Length of longest common subsequence
6UGU_1,8YEF_1
124
6
6UGU_1,8PKY_1
154
3
8YEF_1,8PKY_1
140
3
Newick tree
[
8PKY_1:77.05,
[
6UGU_1:62,8YEF_1:62
]:15.05
]
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 \((0.85)(0.8)(\frac{346
}{\log_{20}
346}-\frac{120}{\log_{20}120})=69.4\)
Status
Protein1
Protein2
d
d1/2
Query variables
6UGU_1
8YEF_1
83
61.5
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]