CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5NDE_1 4HNH_1 4TOQ_1 Letter Amino acid
25 16 13 V Valine
20 18 23 L Leucine
12 16 25 T Threonine
18 10 21 D Aspartic acid
1 0 6 C Cysteine
3 9 11 Q Glutamine
18 15 29 G Glycine
6 6 3 H Histidine
15 19 27 A Alanine
14 10 12 P Proline
16 13 24 S Serine
6 9 14 Y Tyrosine
7 5 2 M Methionine
12 8 11 F Phenylalanine
4 2 5 W Tryptophan
8 12 6 R Arginine
12 10 13 N Asparagine
14 16 5 E Glutamic acid
10 17 15 I Isoleucine
29 10 8 K Lycine 

5NDE_1|Chains A, B|Beta-lactamase IMP-1|Pseudomonas aeruginosa (287)
>4HNH_1|Chains A, B|NAD-dependent epimerase/dehydratase|Veillonella parvula (479436)
>4TOQ_1|Chains A, B, C, D|Class III chitinase|Punica granatum (22663)
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 \(w=f(c)\)
5NDE , Knot 110 250 0.81 40 160 240 
GPKSSDHVDLPYNLTATKIDSDVFVVTDRDFYSSNVLVAKMLDGTVVIVSSPFENLGTQTLMDWVAKTMKPKKVVAINTHFHLDGTGGNEIYKKMGAETWSSDLTKQLRLEENKKDRIKAAEFYKNEDLKRRILSSHPVPADNVFDLKQGKVFSFSNELVEVSFPGPAHSPDNVVVYFPKKKLLFGGCMIKPKELGYLGDANVKAWPDSARRLKKFDAKIVIPGHGEWGGPEMVNKTIKVAEKAVGEMRL
4HNH , Knot 105 221 0.85 38 160 216 
SNAMYKYITILGAAGQIAQKLTATLLTYTDMHITLYGRQLKTRIPPEIIDHERVTVIEGSFQNPGKLEQAVTNAEVVFVGAMESGSDMASIVKALSRKNIRRVIGVSMAGLSGEFPVALEKWTFDNLPISYVQGERQARNVLRESNLNYTILRLTWLYNDPEKTDYELIPEGAQFNDAQVSREAVVKAIFDILHAADETPFHRTSIGVGEPGTHYDKPSFH
4TOQ , Knot 117 273 0.80 40 166 259 
GDIAIYWGQNGGEGTLASTCDTGRYAYVIVSFVTTFGNFRAPVVNLAGHCDPAAGTCTGLSDEIRSCQGKDIKVLMSIGGGAGDYSLVSEADADNFADYLWNNFLGGQSSSRPLGDAVLDGIDFDIELGTTTFYDTLARALSSRSTQAAKVYLTAAPQCPHPDSHLDAALNTGLFDNVWIQFYNNPLAQCQYSSGNTNDILSSWNTWTSSTTAGKIFLGLPAAPEAAGSGYIPPDVLTGQILPQIKTSAKYGGVMLYSKFYDTTYSTTIKDQV

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 \(c\).

\(|P_{f(5NDE_1)}(2) \setminus P_{f(4HNH_1)}(2)|=87\), \(|P_{f(4HNH_1)}(2) \setminus P_{f(5NDE_1)}(2)|=87\). 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 1:1100000101100101001000111100001000011110110101111001100110001101110010100111100010101011001000111001000100010100000001011010000010001100011110011010010110100011010111110010011101100011111011010011011010101110010010010101111101011110110001011001110101
Pair \(Z_2\) Length of longest common subsequence
5NDE_1,4HNH_1 174 4
5NDE_1,4TOQ_1 168 4
4HNH_1,4TOQ_1 158 3

Newick tree

 
[
	5NDE_1:87.57,
	[
		4TOQ_1:79,4HNH_1:79
	]:8.57
]

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 \((0.85)(0.8)(\frac{471 }{\log_{20} 471}-\frac{221}{\log_{20}221})=72.4\)
Status Protein1 Protein2 d d1/2
Query variables 5NDE_1 4HNH_1 91 87
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]