CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4RWX_1 8KCJ_1 3ETO_1 Letter Amino acid
5 10 8 H Histidine
4 1 3 M Methionine
4 5 12 P Proline
5 1 18 S Serine
4 0 18 Q Glutamine
4 0 13 N Asparagine
8 17 16 E Glutamic acid
2 2 7 Y Tyrosine
10 51 18 A Alanine
1 0 20 C Cysteine
7 3 5 I Isoleucine
8 32 19 L Leucine
6 2 6 K Lycine
7 1 11 F Phenylalanine
3 15 8 R Arginine
9 11 18 G Glycine
11 5 5 T Threonine
0 1 4 W Tryptophan
10 16 15 V Valine
6 8 18 D Aspartic acid 

4RWX_1|Chains A, B, C|Lmo2692 protein|Listeria monocytogenes (169963)
>8KCJ_1|Chain A|De novo design protein -N7|synthetic construct (32630)
>3ETO_1|Chains A, B|Neurogenic locus notch homolog protein 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 \(w=f(c)\)
4RWX , Knot 58 114 0.80 38 91 110 
MKLIFAIVQDQDSNRLSDALTKGNFGATKLATTGGFLKAGNTTFIIGTEDERVEDALAIIKENCKAREQMMTPSASLGVTVDTYVPYPIEVQVGGATVFVMPVESFHHFLEHHH
8KCJ , Knot 66 181 0.63 34 75 133 
GLEAAVDAAYEILLEELEKHGVRTIVVVGTGELALVLALAGVRLARERGVKTIVLVRDAAAAHRLLAALAAALGLPAPASADAAALAAADAALWAEHGLRVRVADLTDPAALRAALEALFAEHGRDDTLVLPAGEAALAALEPVLRELGLEEMAAVAREVYARLRAALAAARALEHHHHHH
3ETO , Knot 109 242 0.82 40 170 223 
GEEACELPECQEDAGNKVCSLQCNNHACGWDGGDCSLNFNDPWKNCTQSLQCWKYFSDGHCDSQCNSAGCLFDGFDCQRAEGQCNPLYDQYCKDHFSDGHCDQGCNSAECEWDGLDCAEHVPERLAAGTLVVVVLMPPEQLRNSSFHFLRELSRVLHTNVVFKRDAHGQQMIFPYYGMDVRGSIVYLEIDNRQCVQASSQCFQSATDVAAFLGALASLGSLNIPYKIEAVQSETVEPPPPAQ

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 \(c\).

\(|P_{f(4RWX_1)}(2) \setminus P_{f(8KCJ_1)}(2)|=65\), \(|P_{f(8KCJ_1)}(2) \setminus P_{f(4RWX_1)}(2)|=49\). 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 1:101111110000000100110010111001100111101100011110000010011111000001000110101011101000110110101111011111100100110000
Pair \(Z_2\) Length of longest common subsequence
4RWX_1,8KCJ_1 114 5
4RWX_1,3ETO_1 171 4
8KCJ_1,3ETO_1 159 4

Newick tree

 
[
	3ETO_1:89.46,
	[
		4RWX_1:57,8KCJ_1:57
	]:32.46
]

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 \((0.85)(0.8)(\frac{295 }{\log_{20} 295}-\frac{114}{\log_{20}114})=56.6\)
Status Protein1 Protein2 d d1/2
Query variables 4RWX_1 8KCJ_1 58 52.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]