CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8YKH_1 2DJQ_1 9BKC_1 Letter Amino acid
8 2 5 F Phenylalanine
15 3 18 A Alanine
6 5 3 N Asparagine
8 3 6 D Aspartic acid
4 1 0 C Cysteine
7 3 8 E Glutamic acid
7 0 1 H Histidine
6 1 1 W Tryptophan
2 0 1 M Methionine
11 4 11 P Proline
37 10 13 S Serine
19 0 10 T Threonine
15 2 10 Q Glutamine
33 11 14 G Glycine
19 5 22 L Leucine
7 4 7 K Lycine
13 4 18 V Valine
11 4 8 R Arginine
11 4 6 I Isoleucine
12 2 3 Y Tyrosine 

8YKH_1|Chain A|NT-108 scFv|Homo sapiens (9606)
>2DJQ_1|Chain A|SH3 domain containing ring finger 2|Mus musculus (10090)
>9BKC_1|Chains A, B, C, D, E, F|Rid family protein PFL1385|Pseudomonas fluorescens (294)
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 \(w=f(c)\)
8YKH , Knot 105 251 0.77 40 154 222 
EIVLTQSPGTLSLSPGERATLSCRASQSVSSTFLAWYQQKPGQAPRLLIYGASYMATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSLTFGGGTKLEIKGGGGSGGGGSGGGGSQVQLQQSGPGLVKPSQTLSLTCSISGDSVSSNSAAWNWIRQSPSRGLEWLGRTYYRSKWYNDYAGTVKSRIAINPDTSKNQFSLHLNSVTPEDTAVYFCARVISVAGYAFDIWGQGTMVTVSSHHHHHH
2DJQ , Knot 38 68 0.78 34 56 62 
GSSGSSGPRAKALCNYRGKNPGDLKFNKGDVILLRRQLDENWYQGEINGVSGIFPASSVEVISGPSSG
9BKC , Knot 76 165 0.78 38 115 160 
MSLKSTVVGLGLLFAASSSWAAGIQRVPSSYPNSPILQSVTLPANSEVTYLSGLLPDPVDPKASKEQIHAEGNTEAQARVVLRKVETILASQGLTLGDVVQLRIYLVGDPALGGKLDFDGLQVAFREFFGTQKQPLKPARTTVQVAGLVLPGALIEVETVAARAR

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 \(c\).

\(|P_{f(8YKH_1)}(2) \setminus P_{f(2DJQ_1)}(2)|=124\), \(|P_{f(2DJQ_1)}(2) \setminus P_{f(8YKH_1)}(2)|=26\). 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 1:01110001101010110010100010001000111100001101101110110011011100101010100101010010100111000000100101111001010111101111011110010100011111010001010001010010000111011000100110111000000010000110100011101000000101010010100011010101101110110111010110100000000
Pair \(Z_2\) Length of longest common subsequence
8YKH_1,2DJQ_1 150 3
8YKH_1,9BKC_1 151 3
2DJQ_1,9BKC_1 125 3

Newick tree

 
[
	8YKH_1:79.04,
	[
		2DJQ_1:62.5,9BKC_1:62.5
	]:16.54
]

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 \((0.85)(0.8)(\frac{319 }{\log_{20} 319}-\frac{68}{\log_{20}68})=79.8\)
Status Protein1 Protein2 d d1/2
Query variables 8YKH_1 2DJQ_1 95 60
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]