CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5QHA_1 1ZGV_1 8JXG_1 Letter Amino acid
14 12 15 A Alanine
4 8 0 C Cysteine
3 7 4 M Methionine
9 10 5 F Phenylalanine
4 16 28 S Serine
11 11 15 T Threonine
10 21 18 R Arginine
13 19 22 D Aspartic acid
11 19 42 E Glutamic acid
11 24 18 G Glycine
12 22 39 K Lycine
18 17 10 V Valine
6 11 14 N Asparagine
7 8 7 Q Glutamine
9 5 18 H Histidine
0 9 6 W Tryptophan
9 17 6 I Isoleucine
23 25 49 L Leucine
14 15 7 P Proline
8 11 9 Y Tyrosine 

5QHA_1|Chain A|Peroxisomal coenzyme A diphosphatase NUDT7|Homo sapiens (9606)
>1ZGV_1|Chain A|Thrombin|Homo sapiens (9606)
>8JXG_1|Chain A[auth D]|rat RAP|Rattus norvegicus (10116)
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 \(w=f(c)\)
5QHA , Knot 92 196 0.82 38 147 187 
SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
1ZGV , Knot 130 287 0.85 40 195 272 
DCGLRPLFEKKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
8JXG , Knot 102 332 0.59 38 135 220 
GPLGSHGGKYSREKNEPEMAAKRESGEEFRMEKLNQLWEKAKRLHLSPVRLAELHSDLKIQERDELNWKKLKVEGLDGDGEKEAKLVHNLNVILARYGLDGRKDTQTVHSNALNEDTQDELGDPRLEKLWHKAKTSGKFSSEELDKLWREFLHYKEKIHEYNVLLDTLSRAEEGYENLLSPSDMTHIKSDTLASKHSELKGRKDTQTVHSNALNEDTQDELGDPRLEKLWHKAKTSGKFSSEELDKLWREFLHYKEKIHEYNVLLDTLSRAEEGYENLLSPSDMTHIKSDTLASKHSELKLLEEKTKELGYKVKKHLQDLSSRVSRARHNEL

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 \(c\).

\(|P_{f(5QHA_1)}(2) \setminus P_{f(1ZGV_1)}(2)|=74\), \(|P_{f(1ZGV_1)}(2) \setminus P_{f(5QHA_1)}(2)|=122\). 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 1:0110010101000011100001100000111111100101011101000010011101011110001001001101100100011101001011001110110000110111111000101010110100111111101101010000010011001100110000100110001011010111111111100010
Pair \(Z_2\) Length of longest common subsequence
5QHA_1,1ZGV_1 196 4
5QHA_1,8JXG_1 158 5
1ZGV_1,8JXG_1 176 3

Newick tree

 
[
	1ZGV_1:97.39,
	[
		5QHA_1:79,8JXG_1:79
	]:18.39
]

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 \((0.85)(0.8)(\frac{483 }{\log_{20} 483}-\frac{196}{\log_{20}196})=83.5\)
Status Protein1 Protein2 d d1/2
Query variables 5QHA_1 1ZGV_1 106 89.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]