CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5HWN_1 6DJC_1 3BDV_1 Letter Amino acid
15 3 15 R Arginine
7 9 14 Q Glutamine
14 12 10 P Proline
15 9 8 T Threonine
17 5 7 F Phenylalanine
2 3 8 W Tryptophan
40 5 17 A Alanine
21 9 15 E Glutamic acid
33 2 12 G Glycine
16 9 11 I Isoleucine
7 6 5 M Methionine
12 7 3 Y Tyrosine
8 12 3 N Asparagine
15 6 11 D Aspartic acid
5 2 2 C Cysteine
15 12 1 K Lycine
6 1 7 H Histidine
28 13 18 L Leucine
12 2 11 S Serine
23 5 13 V Valine 

5HWN_1|Chains A, B, C, D|Probable 5-dehydro-4-deoxyglucarate dehydratase|Agrobacterium fabrum (strain C58 / ATCC 33970) (176299)
>6DJC_1|Chains A, B|Bromodomain-containing protein 4|Homo sapiens (9606)
>3BDV_1|Chains A, B|Uncharacterized protein DUF1234|Pectobacterium atrosepticum SCRI1043 (218491)
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 \(w=f(c)\)
5HWN , Knot 137 311 0.84 40 194 303 
MDPEQIKTALGSGLLSFPVTHFDAEGRFAADSYREHVEWLAGYKAPVLFAAGGTGEFFSLKPDEIPTIVAAAKEVAGETAIVSGCGYGTEIAVDIARSVEKVGADGILLLPHYLIDAPQEGLYAHIKKVCQSVGIGVMVYNRDNSVLQADTLARLCDECPNLVGFKDGTGDIGLVRQITAKMGDRLMYLGGMPTAELFAEAYLGAGFTTYSSAVFNFVPGLANEFYAALRAGERATCERILVDFFYPFMAIRNRAKGYAVSAVKAGVRLQGFNAGPVRAPLKDLTNEEIGMLEALIGTHKRKAWSHPQFEK
6DJC , Knot 68 132 0.83 40 113 128 
SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMI
3BDV , Knot 90 191 0.82 40 140 184 
GMQTTEIDLRLTEVSQQLTMVLVPGLRDSDDEHWQSHWERRFPHWQRIRQREWYQADLDRWVLAIRRELSVCTQPVILIGHSFGALAACHVVQQGQEGIAGVMLVAPAEPMRFEIDDRIQASPLSVPTLTFASHNDPLMSFTRAQYWAQAWDSELVDVGEAGHINAEAGFGPWEYGLKRLAEFSEILIPNR

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 \(c\).

\(|P_{f(5HWN_1)}(2) \setminus P_{f(6DJC_1)}(2)|=134\), \(|P_{f(6DJC_1)}(2) \setminus P_{f(5HWN_1)}(2)|=53\). 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 1:10100100111011101110010101011100000010111100111111111010110101001101111100111001110101010011101100100111011111100110110011010100100011111110000001101001101000010111100101011110010101100110111110101110101111100000111011111100101110110010000111011011111000101011011011101011011110111001000011110111100000110010100
Pair \(Z_2\) Length of longest common subsequence
5HWN_1,6DJC_1 187 3
5HWN_1,3BDV_1 158 4
6DJC_1,3BDV_1 179 3

Newick tree

 
[
	6DJC_1:95.33,
	[
		5HWN_1:79,3BDV_1:79
	]:16.33
]

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 \((0.85)(0.8)(\frac{443 }{\log_{20} 443}-\frac{132}{\log_{20}132})=93.0\)
Status Protein1 Protein2 d d1/2
Query variables 5HWN_1 6DJC_1 119 84
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]