CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9BEQ_1 3SGE_1 7CIK_1 Letter Amino acid
15 11 8 P Proline
22 30 9 S Serine
16 21 4 T Threonine
11 13 21 V Valine
17 8 10 R Arginine
16 14 16 K Lycine
7 9 3 Y Tyrosine
23 9 17 E Glutamic acid
21 16 10 G Glycine
14 3 9 H Histidine
3 4 0 W Tryptophan
17 7 10 A Alanine
6 9 6 N Asparagine
22 9 4 Q Glutamine
40 18 17 L Leucine
14 2 3 M Methionine
19 8 6 F Phenylalanine
12 14 8 D Aspartic acid
6 5 2 C Cysteine
15 9 10 I Isoleucine 

9BEQ_1|Chain A|Nuclear receptor subfamily 1 group I member 2|Homo sapiens (9606)
>3SGE_1|Chains A[auth I], C[auth L]|Light Chain|Mus musculus (10090)
>7CIK_1|Chains A, B|Flagellar M-ring protein|Aquifex aeolicus (strain VF5) (224324)
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 \(w=f(c)\)
9BEQ , Knot 139 316 0.84 40 202 300 
MGKGHHHHHHGSERTGTQPLGVQGLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITGS
3SGE , Knot 102 219 0.83 40 157 213 
DVVMTQTPLTLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGSHFPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
7CIK , Knot 80 173 0.79 38 115 161 
MNHKVHHHHHHIEGRHMPDDLNAVVTELDKEGVKYKISPDGRTIYVPENVARELRLKLAAKGVPRKGIVGYELFDKSGIVLSRFQQLVNFKRAIEGELAKTIMSLDCVEFARVHIVLPEKSLFIREEEEAKASVFLKLKPGCELTPEQVKAIRNLVSGSVENLKPSQVVVVDD

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 \(c\).

\(|P_{f(9BEQ_1)}(2) \setminus P_{f(3SGE_1)}(2)|=113\), \(|P_{f(3SGE_1)}(2) \setminus P_{f(9BEQ_1)}(2)|=68\). 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 1:1101000000100001001111011000001110011010100100010010010111110010011001011000011010010001001010101010010110001110011001101110110100011011101101100100111000101101111010010100110100101001010001000111100111011101001100101000001110110110100111100011001000111010001000010110011110111110010010100000110100101110111001111010
Pair \(Z_2\) Length of longest common subsequence
9BEQ_1,3SGE_1 181 4
9BEQ_1,7CIK_1 173 6
3SGE_1,7CIK_1 164 3

Newick tree

 
[
	9BEQ_1:90.59,
	[
		7CIK_1:82,3SGE_1:82
	]:8.59
]

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 \((0.85)(0.8)(\frac{535 }{\log_{20} 535}-\frac{219}{\log_{20}219})=90.6\)
Status Protein1 Protein2 d d1/2
Query variables 9BEQ_1 3SGE_1 117 98
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]