CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7JZK_1 9GFW_1 4QJB_1 Letter Amino acid
7 12 11 T Threonine
2 7 1 W Tryptophan
7 22 15 G Glycine
12 18 19 S Serine
9 13 28 E Glutamic acid
7 26 24 L Leucine
6 17 4 P Proline
5 8 9 Y Tyrosine
6 19 13 D Aspartic acid
2 1 7 C Cysteine
3 10 29 N Asparagine
3 11 6 Q Glutamine
4 9 27 I Isoleucine
3 24 24 K Lycine
4 12 12 F Phenylalanine
10 17 22 V Valine
5 13 12 A Alanine
9 7 8 R Arginine
1 12 16 H Histidine
0 2 9 M Methionine 

7JZK_1|Chains A, C|LAIR1 ecotodomain from MGD21 antibody|Homo sapiens (9606)
>9GFW_1|Chain A|Carbonic anhydrase 2|Homo sapiens (9606)
>4QJB_1|Chains A, B|Haloacid dehalogenase-like hydrolase|Plasmodium falciparum (36329)
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 \(w=f(c)\)
7JZK , Knot 52 105 0.76 38 88 101 
TDLPRPSISAEPGTVIPLGSHVTFVCRGPVGVQTFRLERERNYLYSDTEDVSQTSPSESEARFRIDSVNAGNAGLFRCIYYKSRKWSEQSDYLELVVKGEDVTWA
9GFW , Knot 112 260 0.79 40 176 249 
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
4QJB , Knot 129 296 0.82 40 184 287 
MAHHHHHHMHEIVDKNGKKVQKNNLNDEIKIIFTDLDGTLLNSENKVSEQNLESLIRAQEKGIKVVIATGRSIFSVENVIGEHVKKNRISLLPGIYMNGCVTFDEKGSRVIDRIMNNDLKMEIHEFSKQINISKYAIWFCLEKTYCFEINDCIREYMEVEALNPDVIEDNMLEGLTVYKVLFSLPENILENTLKLCREKFSHRINVANTFQSYVELFHQHTNKFEGVKEICKYYNISLNNALAMGDGENDIEMLSGLTHSVGVHNASEKVKNSAAYVGPSNNEHAISHVLKTFCDI

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 \(c\).

\(|P_{f(7JZK_1)}(2) \setminus P_{f(9GFW_1)}(2)|=38\), \(|P_{f(9GFW_1)}(2) \setminus P_{f(7JZK_1)}(2)|=126\). 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 1:001101010101101111100101100111110010100000010000001000010000101010010110111100100000010000001011101001011
Pair \(Z_2\) Length of longest common subsequence
7JZK_1,9GFW_1 164 3
7JZK_1,4QJB_1 178 3
9GFW_1,4QJB_1 178 4

Newick tree

 
[
	4QJB_1:91.21,
	[
		7JZK_1:82,9GFW_1:82
	]:9.21
]

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 \((0.85)(0.8)(\frac{365 }{\log_{20} 365}-\frac{105}{\log_{20}105})=80.0\)
Status Protein1 Protein2 d d1/2
Query variables 7JZK_1 9GFW_1 100 69.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]