CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2KDX_1 7SXG_1 6YXV_1 Letter Amino acid
7 21 18 I Isoleucine
2 17 11 Y Tyrosine
6 13 12 D Aspartic acid
4 12 10 N Asparagine
1 24 14 P Proline
0 2 5 W Tryptophan
8 21 16 A Alanine
6 8 8 C Cysteine
4 3 10 M Methionine
2 16 13 T Threonine
4 21 19 R Arginine
15 21 22 E Glutamic acid
5 17 17 G Glycine
5 7 5 H Histidine
11 41 27 L Leucine
10 19 16 K Lycine
4 16 11 F Phenylalanine
11 23 21 S Serine
2 15 11 Q Glutamine
12 26 16 V Valine 

2KDX_1|Chain A|Hydrogenase/urease nickel incorporation protein hypA|Helicobacter pylori (85962)
>7SXG_1|Chain A|Glycogen synthase kinase-3 alpha|Homo sapiens (9606)
>6YXV_1|Chains A, B, C, D|Focal adhesion kinase 1|Homo sapiens (9606)
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 \(w=f(c)\)
2KDX , Knot 62 119 0.83 38 99 116 
GSMHEYSVVSSLIALCEEHAKKNQAHKIERVVVGIGERSAMDKSLFVSAFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYGVCEKCHSKNVIITQGNEMRLLSLEMLAE
7SXG , Knot 153 343 0.86 40 204 329 
VVATLGQGPERSQEVAYTDIKVIGNGSFGVVYQARLAETRELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDELYLNLVLEYVPETVYRVARHFTKAKLTIPILYVKVYMYQLFRSLAYIHSQGVCHRDIKPQNLLVDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFKSRTPPEAIALCSSLLEYTPSSRLSPLEACAHSFFDELRCLGTQLPNNRPLPPLFNFSAGELSIQPSLNAILIPPHL
6YXV , Knot 126 282 0.84 40 187 269 
GSGSTRDYEIQRERIELGRCIGEGQFGDVHQGIYMSPENPALAVAIKTCKNCTSDSVREKFLQEALTMRQFDHPHIVKLIGVITENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYAYQLSTALAYLESKRFVHRDIAARNVLVSSNDCVKLGDFGLSRYMEDSTYYKASKGKLPIKWMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILEEEKAQQEE

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 \(c\).

\(|P_{f(2KDX_1)}(2) \setminus P_{f(7SXG_1)}(2)|=33\), \(|P_{f(7SXG_1)}(2) \setminus P_{f(2KDX_1)}(2)|=138\). 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 1:10100001100111100001000010010011111100011000111011001000011000111011000101000000011010110011000000001110010010110101110
Pair \(Z_2\) Length of longest common subsequence
2KDX_1,7SXG_1 171 4
2KDX_1,6YXV_1 184 3
7SXG_1,6YXV_1 169 4

Newick tree

 
[
	2KDX_1:90.20,
	[
		7SXG_1:84.5,6YXV_1:84.5
	]:5.70
]

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 \((0.85)(0.8)(\frac{462 }{\log_{20} 462}-\frac{119}{\log_{20}119})=102.\)
Status Protein1 Protein2 d d1/2
Query variables 2KDX_1 7SXG_1 133 87.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]