CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3ELB_1 8WKD_1 6REE_1 Letter Amino acid
8 3 1 C Cysteine
16 6 7 Q Glutamine
27 14 14 G Glycine
15 0 5 H Histidine
7 6 2 M Methionine
9 11 5 N Asparagine
21 8 7 D Aspartic acid
23 19 14 E Glutamic acid
19 11 6 I Isoleucine
21 11 11 T Threonine
18 2 4 Y Tyrosine
19 18 34 A Alanine
23 7 5 R Arginine
22 11 11 L Leucine
17 22 11 K Lycine
31 19 22 V Valine
11 9 12 F Phenylalanine
14 1 13 P Proline
17 13 14 S Serine
3 1 1 W Tryptophan 

3ELB_1|Chain A|Ethanolamine-phosphate cytidylyltransferase|Homo sapiens (9606)
>8WKD_1|Chain A|DUF2121 domain-containing protein|Methanosarcina mazei (2209)
>6REE_15|Chain X[auth R]|Mitochondrial ATP synthase subunit delta|Polytomella sp. Pringsheim 198.80 (37502)
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 \(w=f(c)\)
3ELB , Knot 149 341 0.85 40 219 330 
SMGGRRAVRVWCDGCYDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTVDGRDTYEEVKQAGRYRECKRTQGVSTTDLVGRMLLVTKAHHSSQEMSSEYREYADSFGKCPGGRNPWTGVSQFLQTSQKIIQFASGKEPQPGETVIYVAGAFDLFHIGHVDFLEKVHRLAERPYIIAGLHFDQEVNHYKGKNYPIMNLHERTLSVLACRYVSEVVIGAPYAVTAELLSHFKVDLVCHGKTEIIPDRDGSDPYQEPKRRGIFRQIDSGSNLTTDLIVQRIITNRLEY
8WKD , Knot 88 192 0.80 38 132 186 
ALVIAFIGKNGAVMAGDMREITFEGEKPDREKLEKELYSGSIVTDEEMQKKAEEFGVKITVADCKEKVSERNGVLVGEVSSAEGGVVKKRRLYASAGNFAIAELINTEMTLTSQGKGSNFIAFGNEFTKQVANKCFKDNWTKKSNLQDAVKILILCMETVARKTASVSKQFMIVQTASNADVLKVVEKDRNS
6REE , Knot 94 199 0.83 40 134 190 
MFGLKRAVTVGRRFISTSAARMEAAAPAGPKEFTEVWNKKAPSTLIVPEFPSNYTAVKAVGEGQVHGDAFPVNFYTPHSILSQAQKDTVVLPGVDGYFGVKASHVPTIAQLKPGVVELHSGAESEKFFVSGGFAFVHPNGVTDICVLEAATLDQVDPAAVKSALAAASAAQPTDEFEQAANRAAIELYSALESAVEAKA

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 \(c\).

\(|P_{f(3ELB_1)}(2) \setminus P_{f(8WKD_1)}(2)|=134\), \(|P_{f(8WKD_1)}(2) \setminus P_{f(3ELB_1)}(2)|=47\). 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 1:01110011011001000110010000100101110011111000001100011111000000011011011001111110100100100000010101001010101000000100110000000001100001110111100100000010000000100110011100110110011000001101101001011001101111101101101011001001100101111101000100001000111010000101110001001111110110101100101011001000111000100100010001110010010010001110011000100
Pair \(Z_2\) Length of longest common subsequence
3ELB_1,8WKD_1 181 4
3ELB_1,6REE_1 191 3
8WKD_1,6REE_1 132 4

Newick tree

 
[
	3ELB_1:10.44,
	[
		8WKD_1:66,6REE_1:66
	]:34.44
]

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 \((0.85)(0.8)(\frac{533 }{\log_{20} 533}-\frac{192}{\log_{20}192})=98.5\)
Status Protein1 Protein2 d d1/2
Query variables 3ELB_1 8WKD_1 127 97
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]