6WHD_1|Chains A, B|Thiol:disulfide interchange protein DsbA|Escherichia coli (strain K12) (83333)
>2WIB_1|Chains A, B|FERROUS IRON TRANSPORT PROTEIN B|KLEBSIELLA PNEUMONIAE (573)
>5DIN_1|Chains A, B|Ligand of Numb protein X 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 \(c\).
\(|P_{f(6WHD_1)}(2) \setminus P_{f(2WIB_1)}(2)|=67\),
\(|P_{f(2WIB_1)}(2) \setminus P_{f(6WHD_1)}(2)|=97\).
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 1:100001000001001111110110110110100001001101000100011011010000101111011001001111111111000101111011000001001001001110111010000111001110011100001110101011111110100010101100001011100010010010000
Pair
\(Z_2\)
Length of longest common subsequence
6WHD_1,2WIB_1
164
3
6WHD_1,5DIN_1
170
3
2WIB_1,5DIN_1
172
4
Newick tree
[
5DIN_1:86.63,
[
6WHD_1:82,2WIB_1:82
]:4.63
]
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 \((0.85)(0.8)(\frac{456
}{\log_{20}
456}-\frac{189}{\log_{20}189})=78.2\)
Status
Protein1
Protein2
d
d1/2
Query variables
6WHD_1
2WIB_1
97
84
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]