CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4LJN_1 3NXZ_1 3GNZ_1 Letter Amino acid
4 11 26 A Alanine
9 9 5 R Arginine
4 6 10 N Asparagine
15 1 2 C Cysteine
5 5 14 Q Glutamine
6 13 7 I Isoleucine
11 19 11 L Leucine
9 12 20 S Serine
7 10 14 D Aspartic acid
8 7 14 G Glycine
4 9 8 F Phenylalanine
15 18 13 K Lycine
11 6 15 P Proline
2 1 6 W Tryptophan
0 3 10 Y Tyrosine
3 14 14 V Valine
10 15 5 E Glutamic acid
4 4 5 H Histidine
5 2 4 M Methionine
4 5 10 T Threonine 

4LJN_1|Chain A|Histone acetyltransferase KAT6A|Homo sapiens (9606)
>3NXZ_1|Chains A, B, C, D|Urease accessory protein ureE|Helicobacter pylori (210)
>3GNZ_1|Chain A[auth P]|25 kDa protein elicitor|Pythium aphanidermatum (65070)
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 \(w=f(c)\)
4LJN , Knot 70 136 0.84 38 109 134 
GSHMLELPHEKDKPVAEPIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECKTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRPRKKGRKLLQKK
3NXZ , Knot 83 170 0.83 40 120 163 
MIIERLVGNLRDLNPLDFSVDHVDLEWFETRKKIARFKTRQGKDIAIRLKDAPKLGLSQGDILFKEEKEIIAVNILDSEVIHIQAKSVAEVAKICYEIGNRHAALYYGESQFEFKTPFEKPTLALLEKLGVQNRVLSSKLDSKERLTVSMPHSEPNFKVSLASDFKVVVK
3GNZ , Knot 98 213 0.82 40 151 207 
AVINHDAVPVWPQPEPADATQALAVRFKPQLDVVNGCQPYPAVDPQGNTSGGLKPSGSQAAACRDMSKAQVYSRSGTYNGYYAIMYSWYMPKDSPSTGIGHRHDWENVVVWLDNAASANIVALSASAHSGYKKSFPADKSYLDGITAKISYKSTWPLDHELGFTTSAGKQQPLIQWEQMTQAARDALESTDFGNANVPFKSNFQDKLVKAFFQ

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 \(c\).

\(|P_{f(4LJN_1)}(2) \setminus P_{f(3NXZ_1)}(2)|=70\), \(|P_{f(3NXZ_1)}(2) \setminus P_{f(4LJN_1)}(2)|=81\). 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 1:1001101100000111011110010110000000001001100100100101001010101010101101001000000000001001001110000001101000011100110111100100100010011000
Pair \(Z_2\) Length of longest common subsequence
4LJN_1,3NXZ_1 151 3
4LJN_1,3GNZ_1 174 3
3NXZ_1,3GNZ_1 165 3

Newick tree

 
[
	3GNZ_1:87.65,
	[
		4LJN_1:75.5,3NXZ_1:75.5
	]:12.15
]

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 \((0.85)(0.8)(\frac{306 }{\log_{20} 306}-\frac{136}{\log_{20}136})=52.5\)
Status Protein1 Protein2 d d1/2
Query variables 4LJN_1 3NXZ_1 68 60.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]