CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4FSJ_1 4PGV_1 5XCP_1 Letter Amino acid
20 30 26 L Leucine
34 22 28 V Valine
10 4 22 E Glutamic acid
17 5 8 Q Glutamine
26 11 40 G Glycine
4 2 2 W Tryptophan
4 0 2 C Cysteine
26 6 16 R Arginine
15 6 14 D Aspartic acid
14 23 26 I Isoleucine
9 9 10 M Methionine
20 21 6 F Phenylalanine
30 5 15 P Proline
30 10 21 T Threonine
32 22 37 A Alanine
7 8 7 Y Tyrosine
2 4 11 H Histidine
8 6 21 K Lycine
32 17 27 S Serine
23 6 11 N Asparagine 

4FSJ_1|Chains A, C[auth B], E[auth C]|Capsid protein beta|Flock house virus (12287)
>4PGV_1|Chain A|Uncharacterized protein YetJ|Bacillus subtilis (224308)
>5XCP_1|Chain A[auth X]|Cysteine synthase|Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (71421)
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 \(w=f(c)\)
4FSJ , Knot 154 363 0.83 40 206 351 
MVNNNRPRRQRAQRVVVTTTQTAPVPQQNVPRNGRRRRNRTRRNRRRVRGMNMAALTRLSQPGLAFLKCAFAPPDFNTDPGKGIPDRFEGKVVSRKDVLNQSISFTAGQDTFILIAPTPGVAYWSASVPAGTFPTSATTFNPVNYPGFTSMFGTTSTSRSDQVSSFRYASMNVGIYPTSNLMQFAGSITVWKCPVKLSTVQFPVATDPATSSLVHTLVGLDGVLAVGPDNFSESFIKGVFSQSACNEPDFEFNDILEGIQTLPPANVSLGSTGQPFTMDSGAEATSGVVGWGNMDTIVIRVSAPEGAVNSAILKAWSCIEYRPNPNAMLYQFGHDSPPLDEVALQEYRTVARSLPVAVIAAQN
4PGV , Knot 93 217 0.76 38 135 206 
SNAMQATVHESKQSIMQRILTVFVFTLLIATVGLFIGQFVPVALMLPLSILEVAMIILAFWMRRRKAVGYAFVYTFAFVSGITLFPIVSHYASIAGAYVVLEAFGSTFVIFAVLGTIGAKMKKDLSFLWSFLLVAVLALAVVGIFNIFSPLNSAAMMAYSVIGTIVFSLYILYDLNQIKHRHITEDLIPVMALSLYLDFINLFINLLRFFGILSSDD
5XCP , Knot 147 350 0.82 40 195 326 
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMAIYADNSYSIGNTPLVRLKHFGHNGNVVVKIEGRNPSYSVKCRIGANMVWQAEKDGTLTKGKEIVDATSGNTGIALAYVAAARGYKITLTAPETMSLERKRLLCGLGVNLVLTEGAKGMKGAIAKAEEIVASDPSRYVMLKQFENPANPQIHRETTGPEIWKDTDGKVDVVVAGVGTGGSITGISRAIKLDFGKQITSVAVEPVESPVISQTLAGEEVKPGPHKIQGIGAGFIPKNLDLSIIDRVETVDSDTALATARRLMAEEGILAGISSGAAVAAADRLAKLPEFADKLIVVILPSASERYLSTALFEGIEG

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 \(c\).

\(|P_{f(4FSJ_1)}(2) \setminus P_{f(4PGV_1)}(2)|=118\), \(|P_{f(4PGV_1)}(2) \setminus P_{f(4FSJ_1)}(2)|=47\). 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 1:110000100001001110000011110001100100000000000001011011110010011111100111110100011011100101011000011000101011000111111011110101011110110010010110011100111000000000100100101011101000110111010110011010010111100110001100111101111111001000110111000100010101001101100111101011001011010011010011111101001110101101110011101100100010101110011000111001110000011001111111100
Pair \(Z_2\) Length of longest common subsequence
4FSJ_1,4PGV_1 165 3
4FSJ_1,5XCP_1 137 4
4PGV_1,5XCP_1 162 3

Newick tree

 
[
	4PGV_1:85.71,
	[
		4FSJ_1:68.5,5XCP_1:68.5
	]:17.21
]

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 \((0.85)(0.8)(\frac{580 }{\log_{20} 580}-\frac{217}{\log_{20}217})=103.\)
Status Protein1 Protein2 d d1/2
Query variables 4FSJ_1 4PGV_1 129 101
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]