CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9ICO_1 8CXD_1 6KZI_1 Letter Amino acid
0 3 21 R Arginine
0 7 6 N Asparagine
0 12 19 D Aspartic acid
0 12 24 E Glutamic acid
0 7 18 P Proline
3 9 7 T Threonine
0 14 11 Q Glutamine
0 3 12 H Histidine
0 12 32 L Leucine
0 8 21 S Serine
0 2 7 W Tryptophan
0 21 22 V Valine
1 17 9 A Alanine
2 2 5 C Cysteine
0 5 18 I Isoleucine
0 17 10 K Lycine
0 6 4 M Methionine
1 13 22 G Glycine
0 11 14 F Phenylalanine
0 8 7 Y Tyrosine 

9ICO_1|Chain A[auth T]|DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3')|
>8CXD_1|Chains A, B|Thiol:disulfide interchange protein DsbA|Escherichia coli K-12 (83333)
>6KZI_1|Chain A|Serine/threonine-protein kinase pim-1|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 \(w=f(c)\)
9ICO , Knot 6 7 0.55 8 6 5 
CATCTGT
8CXD , Knot 86 189 0.79 40 134 185 
AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK
6KZI , Knot 126 289 0.82 40 183 272 
GPHMKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK

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 \(c\).

\(|P_{f(9ICO_1)}(2) \setminus P_{f(8CXD_1)}(2)|=6\), \(|P_{f(8CXD_1)}(2) \setminus P_{f(9ICO_1)}(2)|=134\). 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 1:0100010
Pair \(Z_2\) Length of longest common subsequence
9ICO_1,8CXD_1 140 1
9ICO_1,6KZI_1 187 2
8CXD_1,6KZI_1 179 4

Newick tree

 
[
	6KZI_1:97.64,
	[
		9ICO_1:70,8CXD_1:70
	]:27.64
]

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 \((0.85)(0.8)(\frac{196 }{\log_{20} 196}-\frac{7}{\log_{20}7})=68.3\)
Status Protein1 Protein2 d d1/2
Query variables 9ICO_1 8CXD_1 84 44
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: