CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7FRM_1 2CUA_1 7NSZ_1 Letter Amino acid
11 4 11 H Histidine
29 5 12 L Leucine
22 11 20 P Proline
13 10 19 A Alanine
19 5 10 R Arginine
14 13 22 G Glycine
4 2 3 C Cysteine
13 12 9 T Threonine
9 7 7 Y Tyrosine
23 4 10 K Lycine
11 1 7 M Methionine
11 6 6 N Asparagine
30 9 6 E Glutamic acid
18 9 12 I Isoleucine
25 2 13 S Serine
6 1 4 W Tryptophan
17 17 14 V Valine
18 3 13 D Aspartic acid
14 8 10 Q Glutamine
14 6 9 F Phenylalanine 

7FRM_1|Chain A|Tyrosine-protein phosphatase non-receptor type 1|Homo sapiens (9606)
>2CUA_1|Chains A, B|PROTEIN (CUA)|Thermus thermophilus (274)
>7NSZ_1|Chain A[auth AAA]|Isoform A of Peptidoglycan-recognition protein LB|Drosophila melanogaster (7227)
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 \(w=f(c)\)
7FRM , Knot 141 321 0.84 40 205 309 
MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
2CUA , Knot 65 135 0.78 40 107 130 
AYTLATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE
7NSZ , Knot 102 217 0.84 40 157 209 
GPMQQANLGDGVATARLLSRSDWGARLPKSVEHFQGPAPYVIIHHSYMPAVCYSTPDCMKSMRDMQDFHQLERGWNDIGFSFGIGGDGMIYTGRGFNVIGAHAPKYNDKSVGIVLIGDWRTELPPKQMLDAAKNLIAFGVFKGYIDPAYKLLGHRQVRDTECPGGRLFAEISSWPHFTHINDTEGVSSTTAPVVPHVHPQAAAPQKPHQSPPAAPKV

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 \(c\).

\(|P_{f(7FRM_1)}(2) \setminus P_{f(2CUA_1)}(2)|=145\), \(|P_{f(2CUA_1)}(2) \setminus P_{f(7FRM_1)}(2)|=47\). 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 1:101000100100010111100010001001100110110000000000101100001010000000101011010010000110011110011011011100000111110011001010010011000000111000010101100010000010010100100000001101000011011110011011011101000101010011111000111100101011000111100000100101001110100101111001001010011110110111100010001001000010111001111101100110100
Pair \(Z_2\) Length of longest common subsequence
7FRM_1,2CUA_1 192 4
7FRM_1,7NSZ_1 192 3
2CUA_1,7NSZ_1 158 3

Newick tree

 
[
	7FRM_1:10.03,
	[
		2CUA_1:79,7NSZ_1:79
	]:22.03
]

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 \((0.85)(0.8)(\frac{456 }{\log_{20} 456}-\frac{135}{\log_{20}135})=95.6\)
Status Protein1 Protein2 d d1/2
Query variables 7FRM_1 2CUA_1 125 87.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]