CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7QYK_1 2BCX_1 2BZJ_1 Letter Amino acid
5 8 14 F Phenylalanine
8 7 22 V Valine
3 6 8 N Asparagine
3 1 13 H Histidine
11 8 19 I Isoleucine
13 9 38 L Leucine
13 6 21 R Arginine
4 6 11 Q Glutamine
1 11 23 G Glycine
6 4 23 S Serine
6 11 14 A Alanine
12 21 24 E Glutamic acid
7 8 12 K Lycine
2 9 4 M Methionine
0 0 7 W Tryptophan
5 2 7 Y Tyrosine
16 17 20 D Aspartic acid
3 0 6 C Cysteine
6 2 19 P Proline
6 12 8 T Threonine 

7QYK_1|Chain A[auth AAA]|ATPase family AAA domain-containing protein 2|Homo sapiens (9606)
>2BCX_1|Chain A|Calmodulin|Gallus gallus (9031)
>2BZJ_1|Chain A|PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1|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 \(w=f(c)\)
7QYK , Knot 63 130 0.78 38 97 126 
SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
2BCX , Knot 68 148 0.76 36 97 133 
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
2BZJ , Knot 135 313 0.82 40 195 296 
MLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK

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 \(c\).

\(|P_{f(7QYK_1)}(2) \setminus P_{f(2BCX_1)}(2)|=67\), \(|P_{f(2BCX_1)}(2) \setminus P_{f(7QYK_1)}(2)|=67\). 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 1:0100000100101110010001110001011001101001100101100110100110010100010100010010110001100010001100110001011000101110001000100100010000
Pair \(Z_2\) Length of longest common subsequence
7QYK_1,2BCX_1 134 4
7QYK_1,2BZJ_1 182 4
2BCX_1,2BZJ_1 178 3

Newick tree

 
[
	2BZJ_1:96.46,
	[
		7QYK_1:67,2BCX_1:67
	]:29.46
]

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 \((0.85)(0.8)(\frac{278 }{\log_{20} 278}-\frac{130}{\log_{20}130})=46.2\)
Status Protein1 Protein2 d d1/2
Query variables 7QYK_1 2BCX_1 57 54
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]