CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4NZW_1 4HNK_1 2LQO_1 Letter Amino acid
3 3 2 C Cysteine
18 25 4 S Serine
8 9 6 G Glycine
43 17 7 L Leucine
9 3 1 M Methionine
20 7 2 F Phenylalanine
8 5 2 P Proline
14 8 8 V Valine
14 5 4 R Arginine
30 13 5 E Glutamic acid
31 18 5 K Lycine
17 7 10 T Threonine
1 0 1 W Tryptophan
18 20 5 N Asparagine
18 10 4 D Aspartic acid
7 12 7 H Histidine
22 31 4 I Isoleucine
11 14 3 Y Tyrosine
21 6 12 A Alanine
18 6 0 Q Glutamine 

4NZW_1|Chain A|Calcium-binding protein 39|Homo sapiens (9606)
>4HNK_1|Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N|ATP-dependent Clp protease proteolytic subunit|Plasmodium falciparum (36329)
>2LQO_1|Chain A|Putative glutaredoxin Rv3198.1/MT3292|Mycobacterium tuberculosis (1773)
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 \(w=f(c)\)
4NZW , Knot 142 331 0.83 40 197 317 
GAMASHKSPADIVKNLKESMAVLEKQDISDKKAEKATEEVSKNLVAMKEILYGTNEKEPQTEAVAQLAQELYNSGLLSTLVADLQLIDFEGKKDVAQIFNNILRRQIGTRTPTVEYICTQQNILFMLLKGYESPEIALNCGIMLRECIRHEPLAKIILWSEQFYDFFRYVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRFFSEYEKLLHSENYVTKRQSLKLLGELLLDRHNFTIMTKYISKPENLKLMMNLLRDKSRNIQFEAFHVFKVFVANPNKTQPILDILLKNQAKLIEFLSKFQNDRTEDEQFNDEKTYLVKQIRDLK
4HNK , Knot 98 219 0.80 38 145 208 
MGSSHHHHHHSSGRENLYFQGHMSYNEHHKYNINIPSLLLSKRIIFLSSPIYPHISEQIISQLLYLEYESKRKPIHLYINSTGDIDNNKIINLNGITDVISIVDVINYISSDVYTYCLGKAYGIACILASSGKKGYRFSLKNSSFCLNQSYSIIPFNQATNIEIQNKEIMNTKKKVIEIISKNTEKDTNVISNVLERDKYFNADEAVDFKLIDHILEKE
2LQO , Knot 47 92 0.77 38 69 85 
MVTAALTIYTTSWCGYCLRLKTALTANRIAYDEVDIEHNRAAAEFVGSVNGGNRTVPTVKFADGSTLTNPSADEVKAKLVKIAGLEHHHHHH

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 \(c\).

\(|P_{f(4NZW_1)}(2) \setminus P_{f(4HNK_1)}(2)|=102\), \(|P_{f(4HNK_1)}(2) \setminus P_{f(4NZW_1)}(2)|=50\). 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 1:1111000011011001000111100001000010010001000111100110100000100011101100100011100111010110101000110110011000110001010010000011111101000101110011110001000111011110001001100101001011001110100110000110101100000011000001100000100000101110111000010110001001001011101100000010101101101111010000111011100010110110010000000001000000110010010
Pair \(Z_2\) Length of longest common subsequence
4NZW_1,4HNK_1 152 3
4NZW_1,2LQO_1 188 3
4HNK_1,2LQO_1 164 6

Newick tree

 
[
	2LQO_1:91.91,
	[
		4NZW_1:76,4HNK_1:76
	]:15.91
]

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 \((0.85)(0.8)(\frac{550 }{\log_{20} 550}-\frac{219}{\log_{20}219})=94.7\)
Status Protein1 Protein2 d d1/2
Query variables 4NZW_1 4HNK_1 119 97.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]