CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6CTH_1 1QXB_1 5MBL_1 Letter Amino acid
5 4 14 C Cysteine
5 0 6 Q Glutamine
16 0 14 I Isoleucine
28 0 22 S Serine
5 0 8 W Tryptophan
23 0 11 K Lycine
12 0 7 F Phenylalanine
11 0 15 P Proline
38 0 11 L Leucine
21 2 14 A Alanine
17 0 9 R Arginine
14 0 11 N Asparagine
14 0 13 D Aspartic acid
22 0 17 E Glutamic acid
23 4 31 G Glycine
9 0 9 H Histidine
8 0 4 M Methionine
6 2 11 T Threonine
10 0 13 Y Tyrosine
22 0 16 V Valine 

6CTH_1|Chain A|Concanavalin A-like lectin protein kinase family protein|Theobroma cacao (3641)
>1QXB_1|Chains A, B|5'-d(CpGpCpGpApApTpTpCpGpCpG)-3'|
>5MBL_1|Chain A|Cathepsin B|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 \(w=f(c)\)
6CTH , Knot 139 309 0.86 40 196 299 
SMRKFSLNELAKVTSNFNAENKLGEGGFGSVYRGFLRDSDTYIAVKKVSRASKQGIKEYASEVKIISRLRHKNLVKLIGWCHERGELMLVYEFMANGSLDSHIFKGKSLLTWEVRYRIVKDLASALLYLHEEGDHCVLHRDIKTSNIMLDSSFNAKLGDFGLARLVDHAKGLKKTLLAGTVGYMAPECLSSGKASKESDVYSFGVVALEIASGRRSIEPKFEESEALLLVPWVWESYGNERILDIADRKLGMAFDPKQLECLVMVGLWCAHPSHNLRPSIRQVIQVLNFEAPLPNLPGSMPIPNYNDVQ
1QXB , Knot 6 12 0.41 8 7 8 
CGCGAATTCGCG
5MBL , Knot 115 256 0.83 40 178 250 
LKLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD

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 \(c\).

\(|P_{f(6CTH_1)}(2) \setminus P_{f(1QXB_1)}(2)|=196\), \(|P_{f(1QXB_1)}(2) \setminus P_{f(6CTH_1)}(2)|=7\). 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 1:010010100110100010100011011110100111000000111001001000110001001011001000011011110000101111001110101000110100110101000110011011101000100011000100001110001010110111101100101100011110110111001001010000010011111101101000101010000111111111000100011011000111110100100111111101010001010100110110101111011101111000010
Pair \(Z_2\) Length of longest common subsequence
6CTH_1,1QXB_1 203 1
6CTH_1,5MBL_1 178 3
1QXB_1,5MBL_1 177 2

Newick tree

 
[
	6CTH_1:97.66,
	[
		5MBL_1:88.5,1QXB_1:88.5
	]:9.16
]

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 \((0.85)(0.8)(\frac{321 }{\log_{20} 321}-\frac{12}{\log_{20}12})=103.\)
Status Protein1 Protein2 d d1/2
Query variables 6CTH_1 1QXB_1 137 71
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]