CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3QQH_1 2VJC_1 7ECT_1 Letter Amino acid
17 34 21 F Phenylalanine
17 22 20 T Threonine
4 14 8 W Tryptophan
10 17 12 Y Tyrosine
9 16 17 Q Glutamine
21 25 27 K Lycine
5 15 8 M Methionine
10 14 6 H Histidine
15 43 30 S Serine
19 24 59 A Alanine
16 26 22 D Aspartic acid
18 34 30 E Glutamic acid
8 35 19 N Asparagine
3 8 5 C Cysteine
23 40 36 V Valine
40 49 32 L Leucine
21 32 16 P Proline
16 24 20 R Arginine
18 44 50 G Glycine
16 21 22 I Isoleucine 

3QQH_1|Chain A|Cyclin-dependent kinase 2|Homo sapiens (9606)
>2VJC_1|Chains A, B|ACETYLCHOLINESTERASE|TORPEDO CALIFORNICA (7787)
>7ECT_1|Chains A, B, C|Glutamate dehydrogenase|Aspergillus terreus (33178)
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 \(w=f(c)\)
3QQH , Knot 136 306 0.84 40 194 292 
GPLGSPEFMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
2VJC , Knot 216 537 0.84 40 266 516 
DDHSELLVNTKSGKVMGTRVPVLSSHISAFLGIPFAEPPVGNMRFRRPEPKKPWSGVWNASTYPNNCQQYVDEQFPGFSGSEMWNPNREMSEDCLYLNIWVPSPRPKSTTVMVWIYGGGFYSGSSTLDVYNGKYLAYTEEVVLVSLSYRVGAFGFLALHGSQEAPGNVGLLDQRMALQWVHDNIQFFGGDPKTVTIFGESAGGASVGMHILSPGSRDLFRRAILQSGSPNCPWASVSVAEGRRRAVELGRNLNCNLNSDEELIHCLREKKPQELIDVEWNVLPFDSIFRFSFVPVIDGEFFPTSLESMLNSGNFKKTQILLGVNKDEGSFFLLYGAPGFSKDSESKISREDFMSGVKLSVPHANDLGLDAVTLQYTDWMDDNNGIKNRDGLDDIVGDHNVICPLMHFVNKYTKFGNGTYLYFFNHRASNLVWPEWMGVIHGYEIEFVFGLPLVKELNYTAEEEALSRRIMHYWATFAKTGNPNEPHSQESKWPLFTTKEQKFIDLNTEPMKVHQRLRVQMCVFWNQFLPKLLNATAC
7ECT , Knot 188 460 0.83 40 220 424 
MSNLPVEPEFEQAYKELASTLENSTLFQKNPEYRKALAVVSVPERVIQFRVVWENDKGEVQVNRGFRVQFNSALGPYKGGLRFHPSVNLSILKFLGFEQIFKNALTGLNMGGGKGGSDFDPKGKSDSEIRRFCVAFMTELCRHIGADTDVPAGDIGVTGREIGYLFGQYRKLRNSWEGVLTGKGGSWGGSLIRPEATGYGVVYYVEHMIAHATNGAESFAGKRVAISGSGNVAQYAALKVIELGGRVVSLSDSQGSLIVKDTAKDSFTPAEIDAIAALKVDRKQIAELVTDAAFADKFTYLPGQRPWVHVGAVDVALPSATQNEVSGEEAQALIAAGCKFIAEGSNMGCTQAAIDAFEAHREANKGAAAIWYAPGKAANAGGVAVSGLEMAQNSARLSWTAEEVDARLKDIMKSCFQNGLDTAKEYATPADGILPSLVTGSNIAGFTKVAAAMKDQGDWW

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 \(c\).

\(|P_{f(3QQH_1)}(2) \setminus P_{f(2VJC_1)}(2)|=45\), \(|P_{f(2VJC_1)}(2) \setminus P_{f(3QQH_1)}(2)|=117\). 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 1:111101011001001001101001110010001010111100101000001110011001011001001011011011000001011101100010011010110111111100011011011110000011000101001110001110110111101111110000001101100110111100000011011011011101100011111000100110110011010011111100110001011011000100111110001001100110001000101011110111001001110101
Pair \(Z_2\) Length of longest common subsequence
3QQH_1,2VJC_1 162 4
3QQH_1,7ECT_1 170 5
2VJC_1,7ECT_1 166 4

Newick tree

 
[
	7ECT_1:84.98,
	[
		3QQH_1:81,2VJC_1:81
	]:3.98
]

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 \((0.85)(0.8)(\frac{843 }{\log_{20} 843}-\frac{306}{\log_{20}306})=145.\)
Status Protein1 Protein2 d d1/2
Query variables 3QQH_1 2VJC_1 188 145
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]