CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2FRE_1 7MKX_1 6ZYD_1 Letter Amino acid
12 21 15 K Lycine
13 20 10 P Proline
3 10 11 Y Tyrosine
11 23 22 V Valine
21 19 21 A Alanine
6 8 17 N Asparagine
18 40 33 L Leucine
6 4 5 W Tryptophan
16 16 14 D Aspartic acid
0 3 3 C Cysteine
8 16 45 I Isoleucine
11 16 24 F Phenylalanine
15 15 21 S Serine
4 9 12 Q Glutamine
13 18 24 G Glycine
5 5 10 M Methionine
7 17 22 T Threonine
9 16 19 R Arginine
12 17 13 E Glutamic acid
10 10 10 H Histidine 

2FRE_1|Chains A, B|NAD(P)H-flavin oxidoreductase|Agrobacterium tumefaciens str. C58 (176299)
>7MKX_1|Chains A, C|Cyclin-dependent kinase 2|Homo sapiens (9606)
>6ZYD_1|Chains A, B, C, D, E, F, G|Low conductance mechanosensitive channel YnaI,Low conductance mechanosensitive channel YnaI|Escherichia coli (strain K12) (83333)
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 \(w=f(c)\)
2FRE , Knot 97 200 0.85 38 151 194 
MTNSNNRQSEYPVDPLFLDRWSPRAFDGSPMPKEHLLTILDAAHWAPSASNHQPWRFVYAHKDSEDWPLFVELLMEGNQKWAKNASVLLFVISRDHTISHEGEKKPSATHSFDAGAAWFSLAMQAHLLGYHAHGMGGIFKDRIVEKLDIPDGFKVEAGVAIGTLTDKSILPDDLAEREVPSKRVPLADVAFEGRFTGKAD
7MKX , Knot 136 303 0.85 40 193 289 
GPLGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
6ZYD , Knot 151 419 0.72 42 205 340 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMIAELFTNNALNLVIIFGSCAALILMSFWFRRGNRKRKGFLFHAVQFLIYTIIISAVGSIINYVIENYKLKFITPGVIDFICTSLIAVILTIKLFLLINQFEKQQIKKGRDITSARIMSRIIKITIIVVLVLLYGEHFGMSLSGLLTFGGIGGLAVGMAGKDILSNFFSGIMLYFDRPFSIGDWIRSPDRNIEGTVAEIGWRITKITTFDNRPLYVPNSLFSSISVENPGRMTNRRITTTIGLRYEDAAKVGVIVEAVREMLKNHPAIDQRQTLLVYFNQFADSSLNIMVYCFTKTTVWAEWLAAQQDVYLKIIDIVQSHGADFAFPSQTLYMDNITPPEQGRLEHHHHHH

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 \(c\).

\(|P_{f(2FRE_1)}(2) \setminus P_{f(7MKX_1)}(2)|=59\), \(|P_{f(7MKX_1)}(2) \setminus P_{f(2FRE_1)}(2)|=101\). 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 1:10000000000110111100101011010111000110110110111010000110110100000011111011101000110010111111000001000100010100010111111011101011100101111110001100101101101011111101000011100110001100011110111010101010
Pair \(Z_2\) Length of longest common subsequence
2FRE_1,7MKX_1 160 3
2FRE_1,6ZYD_1 176 3
7MKX_1,6ZYD_1 170 4

Newick tree

 
[
	6ZYD_1:88.57,
	[
		2FRE_1:80,7MKX_1:80
	]:8.57
]

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 \((0.85)(0.8)(\frac{503 }{\log_{20} 503}-\frac{200}{\log_{20}200})=87.8\)
Status Protein1 Protein2 d d1/2
Query variables 2FRE_1 7MKX_1 113 91.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]