CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8WYG_1 4NCN_1 8YUN_1 Letter Amino acid
8 10 3 Y Tyrosine
6 35 12 V Valine
6 21 7 R Arginine
2 8 0 C Cysteine
6 19 4 F Phenylalanine
13 9 4 H Histidine
11 49 11 L Leucine
14 33 12 K Lycine
1 1 2 W Tryptophan
11 29 12 A Alanine
4 24 7 Q Glutamine
7 35 16 G Glycine
4 34 9 I Isoleucine
6 16 3 P Proline
1 19 10 T Threonine
5 19 7 N Asparagine
12 24 12 D Aspartic acid
7 38 11 E Glutamic acid
6 10 5 M Methionine
6 24 14 S Serine 

8WYG_1|Chains A, B, C, D|Bromodomain-containing protein 2|Homo sapiens (9606)
>4NCN_1|Chains A, B|Eukaryotic translation initiation factor 5B-like protein|Chaetomium thermophilum var. thermophilum (759272)
>8YUN_1|Chains A, B, C, D, E, F, G, H, I, J, K, L|Hcp1 family type VI secretion system effector|Burkholderia pseudomallei (28450)
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 \(w=f(c)\)
8WYG , Knot 69 136 0.83 40 108 131 
EGDIHMKKGHHHHHHENLYFQGGSGKLSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD
4NCN , Knot 188 457 0.84 40 231 435 
SHMNKDNLRSPICCILGHVDTGKTKLLDKIRQTNVQEGEAGGITQQIGATYFPVEAIKQKTAVVNKDGKFEFKVPGLLIIDTPGHESFSNLRSRGSSLCNIAILVVDIMHGLEPQTIESLRLLRERKTPFVVALNKIDRLYGWKKIENNGFRESFALQNKAVQNEFRNRLDQVKLQFAEQGFNSELFYENKNFARYVSLVPTSAHTGEGIPDMLKLIVQLCQERMASSLMYLSELQATVLEVKAIEGFGVTIDVILSNGILREGDRIVLCGLEGPIKTNIRALLTPAPMRELRIKGQYIHHKEVKAAQGVKISAPGLEGAIAGSRLLVVGPDDDEEELEEEVESDLQSLFSRVEKTGKGVSVQASTLGSLEALLDFLKDCKIPVANVGIGPVYKRDVMQCGIMLEKAPDYAVMLCFDVKVDKEAQQYADENGIKIFTADIIYHLFDQFTKHMQEQLE
8YUN , Knot 79 161 0.83 38 125 156 
MAQDIFLKIDGINGESLDDSHKDEIEVLNWNWEIQQESTMHTGSGGGAGKASVKDLTFEHAIDRASPNLMKYALTGKHVDQAVLVMRKAGGNPLEYLKLTMSDVIITRVRPSGSRDDTERSRETVSLSFAKVKQEYVVQNAQGGSGGAVTTSFDIKGNKEA

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 \(c\).

\(|P_{f(8WYG_1)}(2) \setminus P_{f(4NCN_1)}(2)|=32\), \(|P_{f(4NCN_1)}(2) \setminus P_{f(8WYG_1)}(2)|=155\). 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 1:0101010010000000010101101010001000011100110000110111100110101111000001100110100100010000000100111010111000000011000111110010011010010110
Pair \(Z_2\) Length of longest common subsequence
8WYG_1,4NCN_1 187 4
8WYG_1,8YUN_1 149 5
4NCN_1,8YUN_1 166 3

Newick tree

 
[
	4NCN_1:92.57,
	[
		8WYG_1:74.5,8YUN_1:74.5
	]:18.07
]

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 \((0.85)(0.8)(\frac{593 }{\log_{20} 593}-\frac{136}{\log_{20}136})=132.\)
Status Protein1 Protein2 d d1/2
Query variables 8WYG_1 4NCN_1 169 108.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]