3FZB_1|Chains A, B, C, D, E, F, G, H, I, J|Minor tail protein U|Enterobacteria phage lambda (10710)
>4ROG_1|Chain A|D(GGACACGTGGGAG)|null
>1NTC_1|Chains A, B|PROTEIN (NITROGEN REGULATION PROTEIN (NTRC))|Salmonella typhimurium (90371)
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 \(c\).
\(|P_{f(3FZB_1)}(2) \setminus P_{f(4ROG_1)}(2)|=98\),
\(|P_{f(4ROG_1)}(2) \setminus P_{f(3FZB_1)}(2)|=5\).
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 1:10010000101111011000001101101011110010111111010110001001000010101010111110110001011100010111001111001100111010000000011110010100110001
Pair
\(Z_2\)
Length of longest common subsequence
3FZB_1,4ROG_1
103
2
3FZB_1,1NTC_1
121
3
4ROG_1,1NTC_1
74
2
Newick tree
[
3FZB_1:61.25,
[
4ROG_1:37,1NTC_1:37
]:24.25
]
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 \((0.85)(0.8)(\frac{147
}{\log_{20}
147}-\frac{13}{\log_{20}13})=49.6\)
Status
Protein1
Protein2
d
d1/2
Query variables
3FZB_1
4ROG_1
64
34
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)],
\[
\delta=
\alpha \mathrm{min} + (1-\alpha) \mathrm{max}=
\begin{cases}
d &\alpha=0,\\
d_1/2 &\alpha=1/2
\end{cases}
\]