CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6JDG_1 6XNL_1 2PRN_1 Letter Amino acid
5 1 34 A Alanine
0 0 0 C Cysteine
5 0 13 I Isoleucine
5 5 4 K Lycine
4 1 19 Y Tyrosine
2 1 16 F Phenylalanine
3 0 6 W Tryptophan
10 2 8 R Arginine
5 1 29 D Aspartic acid
8 5 8 E Glutamic acid
7 1 0 H Histidine
2 0 1 P Proline
9 0 22 T Threonine
11 3 26 V Valine
7 1 16 N Asparagine
9 1 9 Q Glutamine
15 0 35 G Glycine
7 6 14 L Leucine
3 1 4 M Methionine
4 1 25 S Serine 

6JDG_1|Chains A, B, C, D|Single-stranded DNA-binding protein|Pseudomonas aeruginosa PAO1 (208964)
>6XNL_1|Chain A|GCN4-p1 Peptide with IPF-F16|Saccharomyces cerevisiae (4932)
>2PRN_1|Chain A|PORIN|Rhodobacter blasticus (1075)
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 \(w=f(c)\)
6JDG , Knot 63 121 0.83 38 96 114 
MARGVNKVILVGNVGGDPETRYMPNGNAVTNITLATSESWKDKQTGQQQERTEWHRVVFFGRLAEIAGEYLRKGSQVYVEGSLRTRKWQGQDGQDRYTTEIVVDINGNMQLLGGRHHHHHH
6XNL , Knot 20 30 0.75 28 28 28 
RMKQLEDKVEELLSKFYHLENEVARLKKLV
2PRN , Knot 122 289 0.79 36 150 272 
MISLNGYGRFGLQYVEDRGVGLEDTIISSRLRINIVGTTETDQGVTFGAKLRMQWDDGDAFAGTAGNAAQFWTSYNGVTVSVGNVDTAFDSVALTYDSWMGYEASSFGDAQSSFFWYNSKYDASGALDNYNGIAVTYSISGVNLYLSYVDPDQTVDSSLVTEEFGIAADWSNDMISLAAAYTTDAGGIVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTAGDQVTLYGNYAFGATTVRAYVSDIDRAGADTAYGIGADYQFAEGVKVSGSVQSGFANETVADVGVRFDF

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 \(c\).

\(|P_{f(6JDG_1)}(2) \setminus P_{f(6XNL_1)}(2)|=87\), \(|P_{f(6XNL_1)}(2) \setminus P_{f(6JDG_1)}(2)|=19\). 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 1:1101100111110111010000110101100101100001000001000000010011111011011100100100101010100001010010000000111010101011110000000
Pair \(Z_2\) Length of longest common subsequence
6JDG_1,6XNL_1 106 2
6JDG_1,2PRN_1 148 4
6XNL_1,2PRN_1 150 3

Newick tree

 
[
	2PRN_1:80.40,
	[
		6JDG_1:53,6XNL_1:53
	]:27.40
]

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 \((0.85)(0.8)(\frac{151 }{\log_{20} 151}-\frac{30}{\log_{20}30})=43.3\)
Status Protein1 Protein2 d d1/2
Query variables 6JDG_1 6XNL_1 53 32.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]