CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5RYZ_1 6COR_1 1VWN_1 Letter Amino acid
13 0 6 Y Tyrosine
6 1 0 M Methionine
12 0 2 P Proline
19 1 9 S Serine
14 1 17 A Alanine
8 0 0 C Cysteine
22 1 5 E Glutamic acid
15 0 16 G Glycine
11 0 2 H Histidine
9 0 19 T Threonine
8 1 3 Q Glutamine
13 1 3 I Isoleucine
31 2 7 L Leucine
4 0 6 W Tryptophan
16 0 7 V Valine
18 3 4 R Arginine
10 0 7 N Asparagine
18 1 4 D Aspartic acid
23 3 4 K Lycine
16 2 2 F Phenylalanine 

5RYZ_1|Chain A|Isoform 2 of Band 4.1-like protein 3|Homo sapiens (9606)
>6COR_1|Chain A|Competence-stimulating peptide type 1|Streptococcus pneumoniae (1313)
>1VWN_1|Chain A[auth B]|STREPTAVIDIN|Streptomyces avidinii (1895)
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 \(w=f(c)\)
5RYZ , Knot 130 286 0.85 40 190 277 
SMPKSMQCKVILLDGSEYTCDVEKRSRGQVLFDKVCEHLNLLEKDYFGLTYRDAENQKNWLDPAKEIKKQVRSGAWHFSFNVKFYPPDPAQLSEDITRYYLCLQLRDDIVSGRLPCSFVTLALLGSYTVQSELGDYDPDECGSDYISEFRFAPNHTKELEDKVIELHKSHRGMTPAEAEMHFLENAKKLSMYGVDLHHAKDSEGVEIMLGVCASGLLIYRDRLRINRFAWPKVLKISYKRNNFYIKIRPGEFEQFESTIGFKLPNHRAAKRLWKVCVEHHTFFRLL
6COR , Knot 14 17 0.77 22 16 15 
EMRLSKFFRDAILQRKK
1VWN , Knot 57 123 0.74 36 85 116 
AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP

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 \(c\).

\(|P_{f(5RYZ_1)}(2) \setminus P_{f(6COR_1)}(2)|=179\), \(|P_{f(6COR_1)}(2) \setminus P_{f(5RYZ_1)}(2)|=5\). 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 1:0110010001111010000001000001011100100010110000111000010000011011001000100111010101010110110100010000101010001101011001101111100010001100010001000100101110000010001101000001101101010110010010101101001000011011111010111100001010011110110100000010101011010010001110110001100110101000011011
Pair \(Z_2\) Length of longest common subsequence
5RYZ_1,6COR_1 184 3
5RYZ_1,1VWN_1 187 3
6COR_1,1VWN_1 101 1

Newick tree

 
[
	5RYZ_1:10.05,
	[
		6COR_1:50.5,1VWN_1:50.5
	]:52.55
]

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 \((0.85)(0.8)(\frac{303 }{\log_{20} 303}-\frac{17}{\log_{20}17})=95.8\)
Status Protein1 Protein2 d d1/2
Query variables 5RYZ_1 6COR_1 121 63
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]