CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4NVR_1 6ZZF_1 6IVH_1 Letter Amino acid
13 1 2 Q Glutamine
16 9 4 S Serine
28 6 10 A Alanine
8 10 0 C Cysteine
23 1 1 G Glycine
10 3 7 K Lycine
19 5 6 P Proline
15 5 9 V Valine
17 4 12 R Arginine
13 5 22 E Glutamic acid
21 10 3 T Threonine
5 0 1 W Tryptophan
10 2 4 Y Tyrosine
19 4 11 D Aspartic acid
31 5 17 L Leucine
16 3 8 I Isoleucine
7 3 5 M Methionine
16 3 1 F Phenylalanine
8 2 1 N Asparagine
12 1 2 H Histidine 

4NVR_1|Chains A, B, C, D|Putative acyltransferase|Salmonella enterica (99287)
>6ZZF_1|Chain A|Secreted Ly-6/uPAR-related protein 1|Homo sapiens (9606)
>6IVH_1|Chain A|Segregation and condensation protein A|Thermococcus onnurineus (strain NA1) (523850)
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 \(w=f(c)\)
4NVR , Knot 138 307 0.85 40 193 298 
SNAMSTLIECGASPFIPGFALKDVRLENGLTVRVAIGGSGSPLVLLHGHPQNHTTWRKVAPTLAQNHTVILPDLRGYGDSDKPTSDPAHRTYSKRTMAQDIVMLMDALGFSRFAFVGHDRGGRVGHRLALDYPDRVTCCTFIDIAPTATMYALTDKSFATRYFWWFFLIQPFPLPETMIAHDPAFFLRKHISGQLKIEGATSQEAFNEYLRCYQNPEMIHAICEDYRAAATIDLDDDAADTSARIRCPLQLLWGGLGTVGQLYNVVGTWKEKALNVQGEALPCGHSPQEECPEYFIQKLQSFLHSVL
6ZZF , Knot 47 82 0.84 38 74 80 
MLKCYTCKEPMTSASCRTITRCKPEDTACMTTLVTVEAEYPFNQSPVVTRSCSSSCVATDPDSIGAAHLIFCCFRDLCNSEL
6IVH , Knot 59 126 0.75 38 89 120 
MESRREEEITPVDILLQLVQMGKVDPWNIDIVDLTEKYIERLREMKELDLRVSARAILAASILVRMKSEALLYADEEDEEEKHEEHIRVEVEPLAPPLRRVERYYTFDDLLDALMDALEEAEKRKP

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 \(c\).

\(|P_{f(4NVR_1)}(2) \setminus P_{f(6ZZF_1)}(2)|=150\), \(|P_{f(6ZZF_1)}(2) \setminus P_{f(4NVR_1)}(2)|=31\). 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 1:0011001100110111111110010100110101111101011111010100000100111011000011110101010000100011000000001100111110111100111110001101100111001001000011011101010110000110001111111011111001110011111000101010101100001100010000010110110000011101010001100010100110111111101101001110100011010101110100100001001100100110011
Pair \(Z_2\) Length of longest common subsequence
4NVR_1,6ZZF_1 181 3
4NVR_1,6IVH_1 176 5
6ZZF_1,6IVH_1 125 3

Newick tree

 
[
	4NVR_1:96.54,
	[
		6IVH_1:62.5,6ZZF_1:62.5
	]:34.04
]

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 \((0.85)(0.8)(\frac{389 }{\log_{20} 389}-\frac{82}{\log_{20}82})=94.9\)
Status Protein1 Protein2 d d1/2
Query variables 4NVR_1 6ZZF_1 123 77.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]