CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4QPR_1 3BXO_1 4IXU_1 Letter Amino acid
4 14 11 F Phenylalanine
11 8 18 P Proline
5 17 15 R Arginine
8 17 21 D Aspartic acid
8 19 15 E Glutamic acid
11 24 26 G Glycine
8 12 11 H Histidine
5 2 20 I Isoleucine
4 5 4 M Methionine
7 15 24 S Serine
10 15 16 T Threonine
7 25 24 V Valine
3 1 10 N Asparagine
0 1 5 C Cysteine
6 6 11 K Lycine
2 3 2 W Tryptophan
16 26 23 A Alanine
10 2 11 Q Glutamine
21 20 32 L Leucine
3 7 7 Y Tyrosine 

4QPR_1|Chain A|Sensor protein KdpD|Escherichia coli (83333)
>3BXO_1|Chains A, B|N,N-dimethyltransferase|Streptomyces venezuelae (54571)
>4IXU_1|Chains A, B, C|Arginase-2, mitochondrial|Homo sapiens (9606)
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 \(w=f(c)\)
4QPR , Knot 71 149 0.79 38 114 143 
GAMDLYEMSKALAVGRSPQDIAATSEQFIASTFHARSQVLLPDDNGKLQPLTHPQGMTPWDDAIAQWSFDKGLPAGAGTDTLPGVPYQILPLKSGEKTYGLVVVEPGNLRQLMIPEQQRLLETFTLLVANALERLTKLAAALEHHHHHH
3BXO , Knot 108 239 0.82 40 146 228 
GHMYEVDHADVYDLFYLGRGKDYAAEASDIADLVRSRTPEASSLLDVACGTGTHLEHFTKEFGDTAGLELSEDMLTHARKRLPDATLHQGDMRDFRLGRKFSAVVSMFSSVGYLKTTEELGAAVASFAEHLEPGGVVVVEPWWFPETFADGWVSADVVRRDGRTVARVSHSVREGNATRMEVHFTVADPGKGVRHFSDVHLITLFHQAEYEAAFTAAGLRVEYLEGGPSGRGLFVGVPA
4IXU , Knot 139 306 0.86 40 189 298 
HSVAVIGAPFSQGQKRKGVEHGPAAIREAGLMKRLSSLGCHLKDFGDLSFTPVPKDDLYNNLIVNPRSVGLANQELAEVVSRAVSDGYSCVTLGGDHSLAIGTISGHARHCPDLCVVWVDAHADINTPLTTSSGNLHGQPVSFLLRELQDKVPQLPGFSWIKPCISSASIVYIGLRDVDPPEHFILKNYDIQYFSMRDIDRLGIQKVMERTFDLLIGKRQRPIHLSFDIDAFDPTLAPATGTPVVGGLTYREGMYIAEEIHNTGLLSALDLVEVNPQLATSEEEAKTTANLAVDVIASSFGQTREG

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 \(c\).

\(|P_{f(4QPR_1)}(2) \setminus P_{f(3BXO_1)}(2)|=58\), \(|P_{f(3BXO_1)}(2) \setminus P_{f(4QPR_1)}(2)|=90\). 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 1:11101001001111100100111000011100101000111100010101100101101100111010100111111100011111001111001000011111011010011110000110010111101100100111110000000
Pair \(Z_2\) Length of longest common subsequence
4QPR_1,3BXO_1 148 5
4QPR_1,4IXU_1 163 4
3BXO_1,4IXU_1 137 3

Newick tree

 
[
	4QPR_1:80.71,
	[
		3BXO_1:68.5,4IXU_1:68.5
	]:12.21
]

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 \((0.85)(0.8)(\frac{388 }{\log_{20} 388}-\frac{149}{\log_{20}149})=71.9\)
Status Protein1 Protein2 d d1/2
Query variables 4QPR_1 3BXO_1 90 72
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]