CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6WLX_1 8ONJ_1 9GZK_1 Letter Amino acid
26 16 18 P Proline
11 6 43 N Asparagine
15 9 9 H Histidine
16 25 47 I Isoleucine
17 14 60 K Lycine
10 10 28 F Phenylalanine
3 1 11 W Tryptophan
8 9 25 Y Tyrosine
30 16 34 V Valine
27 16 25 R Arginine
16 8 46 D Aspartic acid
3 4 1 C Cysteine
22 25 51 E Glutamic acid
23 23 38 G Glycine
36 31 55 L Leucine
23 19 37 S Serine
9 19 35 T Threonine
22 13 33 A Alanine
15 6 16 Q Glutamine
14 7 12 M Methionine 

6WLX_1|Chain A|Serine/threonine-protein kinase PAK 4|Homo sapiens (9606)
>8ONJ_1|Chains A, B|Aminotransferase class IV|Aminobacterium colombiense (81468)
>9GZK_1|Chains A, B, C, D, E, F|Glycosyltransferase|Listeria monocytogenes (1639)
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 \(w=f(c)\)
6WLX , Knot 149 346 0.84 40 201 332 
MGSSHHHHHHSSGLVPRGSHMENLYFQGARARQENGMPEKPPGPRSPQREPQRVSHEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQNRTR
8ONJ , Knot 125 277 0.84 40 174 267 
GHMNLCYIDGKFLPLEEAKLPVTDLIIQRGVGVFETISTHSRRPLMLTPHLKRLEGSATASSIVMPATLDEMARIIREGIKKMGCETMVLPYITGGDSFGKDHLFSSSRYFVIFEEIRKPDPILYEKGVALHPINAERYLPSTKSINYMLSFTGQRDSKGAYEILYCPEGEIVEGSHSTFFLIKNGHLITAPTSRALSGTTRQIVLELARRGNIQVEERCPLLTELPEAEEAFITGTVKELLPVVRIGDQIIGNGVPGKLTKHLHQVYLSSIVEWLE
9GZK , Knot 245 624 0.84 40 267 573 
GMRNLKDRVLNSLKGNKKDIKISVVVPTYNTELEGLKNLMASIDKQTMNPDEYELVFVDDGSTTDTYERLQEFAETRPNMTVKQIENSGWGSRPRNIATKMAKGEYILYLDHDDTVFPETFERVYNFGKENNLDVVSGKEVRTNGWSWGWKQFSENNPHAEEMGIECLLPMTPHKFYKREFLLENDITFDDGARVLWEDVYFNSKAFIHGAKVGILADYPTYYWIATGANNSSSFGRDPHEKWNQINKLFNFFKDNIKEQRDLDFMLTHWYRSRVLGILGQWLLKNNNERIDIEFNYAKKLAEELIPAYISENLDKNNQVKDYLLRQGDLDSLKKLAQIDAGITALSYVEDAYFKEDKLFFKTSTKMTYEDKEDFFIEKTADRMERILPEEIKSKLPKEFFDYSDDLAEFTYEPSIKGRNSRATWKIDGSTSNVEVVNKKANLYKIEGEMSFSVQINDYILDAADKKQPWDIATRFTGLGYTSHRALTIGKILIKTALINNKTMIVYKNASGLISLDVGSSVRSIVEDSGVKREQILIDKTSGKVTIPLNEIHVFGESLIEGNAELKPVGISDADPINVKAKLIGEANKARVEVLLGDEKLSGEYHLVTNIQGKKDKQQIKITL

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 \(c\).

\(|P_{f(6WLX_1)}(2) \setminus P_{f(8ONJ_1)}(2)|=90\), \(|P_{f(8ONJ_1)}(2) \setminus P_{f(6WLX_1)}(2)|=63\). 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 1:1100000000001111010010010101101000011100111100100010010000101110111011010001001101101001110110100010111100101000000011100111100000001101000011100111110110111100110000100001111011110110110101110001000011100010101001110101000110000111010111101100110110101101111110110101101001110110110001110100100101010111001110011001011011001111011111011111000000
Pair \(Z_2\) Length of longest common subsequence
6WLX_1,8ONJ_1 153 3
6WLX_1,9GZK_1 164 4
8ONJ_1,9GZK_1 163 4

Newick tree

 
[
	9GZK_1:83.42,
	[
		6WLX_1:76.5,8ONJ_1:76.5
	]:6.92
]

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 \((0.85)(0.8)(\frac{623 }{\log_{20} 623}-\frac{277}{\log_{20}277})=96.9\)
Status Protein1 Protein2 d d1/2
Query variables 6WLX_1 8ONJ_1 123 109
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]