CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7JWW_1 3MFE_1 6EHG_1 Letter Amino acid
38 34 30 A Alanine
48 28 46 G Glycine
9 5 12 M Methionine
18 5 36 Q Glutamine
38 8 39 K Lycine
30 16 49 S Serine
22 6 24 F Phenylalanine
28 11 48 T Threonine
7 1 4 W Tryptophan
17 13 28 R Arginine
19 4 23 N Asparagine
26 19 27 D Aspartic acid
32 13 41 E Glutamic acid
8 8 10 H Histidine
16 9 23 Y Tyrosine
38 19 73 V Valine
11 0 3 C Cysteine
35 15 34 I Isoleucine
37 18 55 L Leucine
24 7 38 P Proline 

7JWW_1|Chain A|Retinal dehydrogenase 1|Homo sapiens (9606)
>3MFE_1|Chains A[auth 2], B[auth C], C[auth E], E[auth H], F[auth J], G[auth L], H[auth N], I[auth P], J[auth R], L[auth T], M[auth X], N[auth Z]|Proteasome subunit beta|Mycobacterium tuberculosis (1773)
>6EHG_1|Chain A|Complement C3|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 \(w=f(c)\)
7JWW , Knot 205 501 0.84 40 256 471 
MSSSGTPDLPVLLTDLKIQYTKIFINNEWHDSVSGKKFPVFNPATEEELCQVEEGDKEDVDKAVKAARQAFQIGSPWRTMDASERGRLLYKLADLIERDRLLLATMESMNGGKLYSNAYLSDLAGCIKTLRYCAGWADKIQGRTIPIDGNFFTYTRHEPIGVCGQIIPWNFPLVMLIWKIGPALSCGNTVVVKPAEQTPLTALHVASLIKEAGFPPGVVNIVPGYGPTAGAAISSHMDIDKVAFTGSTEVGKLIKEAAGKSNLKRVTLELGGKSPCIVLADADLDNAVEFAHHGVFYHQGQCCIAASRIFVEESIYDEFVRRSVERAKKYILGNPLTPGVTQGPQIDKEQYDKILDLIESGKKEGAKLECGGGPWGNKGYFVQPTVFSNVTDEMRIAKEEIFGPVQQIMKFKSLDDVIKRANNTFYGLSAGVFTKDIDKAITISSALQAGTVWVNCYGVVSAQCPFGGFKMSGNGRELGEYGFHEYTEVKTVTVKISQKNS
3MFE , Knot 108 240 0.82 40 147 227 
XTIVALKYPGGVVMAGDRRSTQGNMISGRDVRKVYITDDYTATGIAGTAAVAVEFARLYAVELEHYEKLEGVPLTFAGKINRLAIMVRGNLAAAMQGLLALPLLAGYDIHASDPQSAGRIVSFDAAGGWNIEEEGYQAVGSGSLFAKSSMKKLYSQVTDGDSGLRVAVEALYDAADDDSATGGPDLVRGIFPTAVIIDADGAVDVPESRIAELARAIIESRSGADTFGSDGGEKHHHHHH
6EHG , Knot 245 643 0.82 40 267 583 
SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNHMGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPGSTVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMGQWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYGKKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGKSLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGSPAYRVPVAVQGEETVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQEISEAEQATRTMQALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLKAGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGSLVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEKADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQP

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 \(c\).

\(|P_{f(7JWW_1)}(2) \setminus P_{f(3MFE_1)}(2)|=138\), \(|P_{f(3MFE_1)}(2) \setminus P_{f(7JWW_1)}(2)|=29\). 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 1:100010101111100101000011100010001010011110110000100100100001001101100110110110010100010110011011000011110100101101000101001110100100011110010100111010110000001111010111101111111101111100100111011000110110110110011111111011110110111110001010011101000110110011100010010101110010111101010011011001110001000111001110001000110001001000111011011100110100000001101100100011010011111100101101011001000101100011111001101001001100100010110111100010011010011011011100011101001111101010100110011000001001010100000
Pair \(Z_2\) Length of longest common subsequence
7JWW_1,3MFE_1 167 5
7JWW_1,6EHG_1 135 4
3MFE_1,6EHG_1 184 3

Newick tree

 
[
	3MFE_1:93.65,
	[
		7JWW_1:67.5,6EHG_1:67.5
	]:26.15
]

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 \((0.85)(0.8)(\frac{741 }{\log_{20} 741}-\frac{240}{\log_{20}240})=139.\)
Status Protein1 Protein2 d d1/2
Query variables 7JWW_1 3MFE_1 181 130
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]