CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8PTQ_1 1NXW_1 1MIE_1 Letter Amino acid
10 3 12 N Asparagine
39 13 16 L Leucine
29 7 32 S Serine
13 5 19 T Threonine
14 6 10 R Arginine
11 4 8 Q Glutamine
10 4 4 M Methionine
20 5 12 P Proline
2 0 3 W Tryptophan
26 8 14 V Valine
25 8 10 A Alanine
17 12 13 E Glutamic acid
25 5 13 G Glycine
19 0 4 H Histidine
11 12 7 I Isoleucine
12 11 10 K Lycine
10 2 9 Y Tyrosine
14 10 9 D Aspartic acid
12 5 9 F Phenylalanine
4 0 5 C Cysteine 

8PTQ_1|Chain A|Monoglyceride lipase|Homo sapiens (9606)
>1NXW_1|Chain A|DNA-binding response regulator|Streptococcus pneumoniae (170187)
>1MIE_1|Chain A[auth L]|IMMUNOGLOBULIN MS5-393|Mus musculus (10090)
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 \(w=f(c)\)
8PTQ , Knot 140 323 0.83 40 192 310 
MGSSHHHHHHSSGENLYFQGMPEESSPRRTPQSIPYQDLPHLVNADGQYLFCRYWAPTGTPKALIFVSHGAGEHSGRYEELARMLMGLDLLVFAHDHVGHGQSEGERMVVSDFHVFVRDVLQHVDSMQKDYPGLPVFLLGHSMGGAIAILTAAERPGHFAGMVLISPLVLANPESATTFKVLAAKVLNSVLPNLSSGPIDSSVLSRNKTEVDIYNSDPLICRAGLKVCFGIQLLNAVSRVERALPKLTVPFLLLQGSADRLCDSKGAYLLMELAKSQDKTLKIYEGAYHVLHKELPEVTNSVFHEINMWVSQRTATAGTASPP
1NXW , Knot 60 120 0.79 34 95 115 
MKKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRRSQ
1MIE , Knot 103 219 0.84 40 161 211 
EIVMTQAAPSVPVTPGESVSISCRSSKSLLHSNGNTYLNWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSETAFTLRTSRVEAEDVGVYYCMQHLEYPFTFGSGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

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 \(c\).

\(|P_{f(8PTQ_1)}(2) \setminus P_{f(1NXW_1)}(2)|=138\), \(|P_{f(1NXW_1)}(2) \setminus P_{f(8PTQ_1)}(2)|=41\). 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 1:11000000000010010101110000100010011000110110101001100011101010111110011100010000110111110111110001101000100111001011100110010010000111111111001111111101100110111111101111101001001011110110011101001110001100000010100001110011101011101101100100111010111111010100100001101110110000001010011001100011010001100101110000101101011
Pair \(Z_2\) Length of longest common subsequence
8PTQ_1,1NXW_1 179 3
8PTQ_1,1MIE_1 167 4
1NXW_1,1MIE_1 164 3

Newick tree

 
[
	8PTQ_1:88.01,
	[
		1MIE_1:82,1NXW_1:82
	]:6.01
]

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 \((0.85)(0.8)(\frac{443 }{\log_{20} 443}-\frac{120}{\log_{20}120})=97.0\)
Status Protein1 Protein2 d d1/2
Query variables 8PTQ_1 1NXW_1 124 84
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]