CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6MEV_1 3TGK_1 5XTK_1 Letter Amino acid
12 4 4 W Tryptophan
21 20 15 V Valine
18 16 14 A Alanine
13 12 12 I Isoleucine
27 19 12 L Leucine
14 5 4 F Phenylalanine
5 2 4 M Methionine
22 17 4 S Serine
12 19 3 N Asparagine
19 15 13 D Aspartic acid
2 12 1 C Cysteine
8 4 3 H Histidine
27 10 8 K Lycine
19 8 8 T Threonine
16 8 5 Y Tyrosine
26 4 9 R Arginine
13 11 6 Q Glutamine
26 9 7 E Glutamic acid
17 23 12 G Glycine
24 13 8 P Proline 

6MEV_1|Chains A, B, C, D, E, F, G, H|Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6|Homo sapiens (9606)
>3TGK_1|Chain A[auth E]|TRYPSIN II, ANIONIC|Rattus norvegicus (10116)
>5XTK_1|Chains A, B|Xanthine phosphoribosyltransferase|Yersinia pestis (632)
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 \(w=f(c)\)
6MEV , Knot 147 341 0.83 40 202 327 
MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESFSLSPAAVADNVERADALQLSVEEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCGEDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDYKVPKFFTDDLFQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRWCLFPTSTPRELIKVTRDEGGNQQDEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVPGGWWHVVLNLDTTIAITQNFASSTNFPVVWHKTVRGRPKLSRKWYRILKQEHPELAVLADSVDLQESTGIASD
3TGK , Knot 106 231 0.83 40 162 222 
EAFPVDDDDKGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEGNEQFVNAAKIIKHPNFDRKTLNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISGWGNTLSSGVNEPDLLQCLDAPLLPQADCEASYPGKITDNMVCVGFLEGGKDSCQGNSGGPVVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN
5XTK , Knot 74 152 0.81 40 116 145 
MNEKYVVTWDMLQIHARKLAQRLLPAEQWKGIIAVSRGGLVPAGILARELGIRYVDTVCISSYDHDNQRDLKVLKRAEGDGEGFIVIDDLVDTGGTATAIREMYPKAHFVTIFAKPAGRPLVDDYVVDIPQNTWIEQPWDMAVTFVAPLSGK

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 \(c\).

\(|P_{f(6MEV_1)}(2) \setminus P_{f(3TGK_1)}(2)|=113\), \(|P_{f(3TGK_1)}(2) \setminus P_{f(6MEV_1)}(2)|=73\). 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 1:10000000100100010101000101000000001010111110010010110101001100000100111110100110100010100100000000100100001001010100010010000000110110000100100001100001101100011001100001100111111100101101011100110111010001011100010011010000110000011011011010001101110101101100110011111111011101000111000110000111110001010101000100110000101111100101000011100
Pair \(Z_2\) Length of longest common subsequence
6MEV_1,3TGK_1 186 3
6MEV_1,5XTK_1 174 3
3TGK_1,5XTK_1 160 3

Newick tree

 
[
	6MEV_1:93.15,
	[
		5XTK_1:80,3TGK_1:80
	]:13.15
]

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 \((0.85)(0.8)(\frac{572 }{\log_{20} 572}-\frac{231}{\log_{20}231})=97.0\)
Status Protein1 Protein2 d d1/2
Query variables 6MEV_1 3TGK_1 127 105.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]