CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3PNO_1 3FFT_1 4FVB_1 Letter Amino acid
8 0 6 H Histidine
17 6 5 I Isoleucine
15 3 4 P Proline
19 4 14 S Serine
4 1 3 W Tryptophan
39 10 17 G Glycine
7 0 5 C Cysteine
6 6 2 M Methionine
9 2 8 Y Tyrosine
14 8 7 N Asparagine
13 5 9 R Arginine
26 8 8 D Aspartic acid
40 15 12 L Leucine
14 11 3 K Lycine
9 5 4 F Phenylalanine
30 16 11 A Alanine
19 11 7 E Glutamic acid
26 5 6 T Threonine
26 10 13 V Valine
16 2 8 Q Glutamine 

3PNO_1|Chains A, B, C, D|PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK|Escherichia coli (83333)
>3FFT_1|Chains A, B|Chemotaxis protein cheY|Escherichia coli (83333)
>4FVB_1|Chain A|2A proteinase|Human enterovirus 71 (39054)
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 \(w=f(c)\)
3PNO , Knot 151 357 0.82 40 203 341 
GSKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGNEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK
3FFT , Knot 63 128 0.79 36 96 121 
ADKELKFLVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM
4FVB , Knot 73 152 0.80 40 117 146 
GSGKFGQQSGAIYVGNFRVVNRHLATHNDWANLVWEDSSRDLLVSSTTAQGCDTIARCNCQTGVYYCNSRRKHYPVSFSKPSLIYVEASEYYPARYQSHLMLAQGHSEPGDAGGILRCQHGVVGIVSTGGNGLVGFADVRDLLWLDEEAMEQ

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 \(c\).

\(|P_{f(3PNO_1)}(2) \setminus P_{f(3FFT_1)}(2)|=145\), \(|P_{f(3FFT_1)}(2) \setminus P_{f(3PNO_1)}(2)|=38\). 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 1:100011001001100011111010101010001101001011111011110111010011001011011101101101100101001100110101101111110000101101001001100011010011100011100010011001110011100111111001001010101100100010011111110011111010101100010111110101110001100100010011001110100000101100001010000000011001001111100111011001011000100000011101000111100001010110101101000011110111001110110
Pair \(Z_2\) Length of longest common subsequence
3PNO_1,3FFT_1 183 4
3PNO_1,4FVB_1 168 4
3FFT_1,4FVB_1 141 3

Newick tree

 
[
	3PNO_1:92.89,
	[
		4FVB_1:70.5,3FFT_1:70.5
	]:22.39
]

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 \((0.85)(0.8)(\frac{485 }{\log_{20} 485}-\frac{128}{\log_{20}128})=106.\)
Status Protein1 Protein2 d d1/2
Query variables 3PNO_1 3FFT_1 133 88.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]