CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8JMQ_1 6QFD_1 5NAL_1 Letter Amino acid
13 3 11 S Serine
9 9 9 R Arginine
2 1 6 Q Glutamine
18 6 7 G Glycine
18 14 14 L Leucine
6 6 6 N Asparagine
18 9 11 V Valine
4 3 7 I Isoleucine
11 0 5 M Methionine
4 1 4 W Tryptophan
4 5 2 Y Tyrosine
7 13 8 A Alanine
14 13 6 D Aspartic acid
3 0 2 C Cysteine
13 15 16 E Glutamic acid
14 6 8 T Threonine
9 1 1 H Histidine
14 6 11 K Lycine
7 3 11 F Phenylalanine
10 2 5 P Proline 

8JMQ_1|Chain A[auth B]|Hinokiresinol synthase beta subunit|Asparagus officinalis (4686)
>6QFD_1|Chains A, B, C, D|DNA-binding protein|Halobacterium salinarum NRC-1 (64091)
>5NAL_1|Chain A[auth B]|Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta|Homo sapiens (9606)
Protein code \(c\) LZ-complexity \(\mathrm{LZ}(w)\) Length \(n=|w|\) \(\frac{\mathrm{LZ}(w)}{n /\log_{20} n}\) \(p_w(1)\) \(p_w(2)\) \(p_w(3)\) Sequence \(w=f(c)\)
8JMQ , Knot 94 198 0.83 40 144 190 
MGSSHHHHHHSSGLVPRGSHMMATVAKELPKVYTENTWMEERNGDRGMLKYPRELDITNVDDGKSWVWHSLVFGSIGRLGMEAPKLMGTTHVEIRGDFKMSKLTPGLKYQAVLLCMKTDGNEGWDSCPLNVELNLPDGTTQKREVDLTKFPTDEFVMMVLGYFEAVESGDITFSVVDTSDCVKKGFVVKDAALRPLPR
6QFD , Knot 57 116 0.77 36 81 109 
PDARSDARDLTAFQKNILTVLGEEARYGLAIKRELEEYYGEEVNHGRLYPNLDDLVNKGLVEKSELDKRTNEYALTNEGFDAVVDDLEWTLSKFVADADRRERVETIVADDAAALE
5NAL , Knot 74 150 0.82 40 118 147 
MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

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 \(c\).

\(|P_{f(8JMQ_1)}(2) \setminus P_{f(6QFD_1)}(2)|=103\), \(|P_{f(6QFD_1)}(2) \setminus P_{f(8JMQ_1)}(2)|=40\). 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 1:110000000000111101001110110011010000011000010011100100101001001001110011110110111011011100010101010100101110001111010001001100011010101101000000101001100011111110101100101010110000010011110011101110
Pair \(Z_2\) Length of longest common subsequence
8JMQ_1,6QFD_1 143 3
8JMQ_1,5NAL_1 138 3
6QFD_1,5NAL_1 133 3

Newick tree

 
[
	8JMQ_1:71.47,
	[
		5NAL_1:66.5,6QFD_1:66.5
	]:4.97
]

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 \((0.85)(0.8)(\frac{314 }{\log_{20} 314}-\frac{116}{\log_{20}116})=61.5\)
Status Protein1 Protein2 d d1/2
Query variables 8JMQ_1 6QFD_1 75 59
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]