1MFC_1|Chain A[auth L]|IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)|Mus musculus (10090)
>5KBW_1|Chains A, B|Riboflavin transporter RibU|Thermotoga maritima (243274)
>8YWQ_1|Chain A[auth H]|Heavy chain of the Fab fragment of anti-IL-6 antibody I9H|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 \(c\).
\(|P_{f(1MFC_1)}(2) \setminus P_{f(5KBW_1)}(2)|=97\),
\(|P_{f(5KBW_1)}(2) \setminus P_{f(1MFC_1)}(2)|=63\).
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 1:01110000110001100101000000101001001011000100110111100000111111010101110011101011010001101011100001111110010111010001010111100001000010110010010111101010101011001100001000000001100010101011000000000100010010001001000
Pair
\(Z_2\)
Length of longest common subsequence
1MFC_1,5KBW_1
160
4
1MFC_1,8YWQ_1
138
4
5KBW_1,8YWQ_1
154
4
Newick tree
[
5KBW_1:81.43,
[
1MFC_1:69,8YWQ_1:69
]:12.43
]
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 \((0.85)(0.8)(\frac{396
}{\log_{20}
396}-\frac{181}{\log_{20}181})=63.9\)
Status
Protein1
Protein2
d
d1/2
Query variables
1MFC_1
5KBW_1
82
74.5
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]