CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6ILA_1 2MJD_1 8BZZ_1 Letter Amino acid
24 6 18 S Serine
23 7 12 T Threonine
1 0 7 W Tryptophan
29 13 19 D Aspartic acid
2 6 1 C Cysteine
45 10 26 L Leucine
24 5 24 K Lycine
13 4 17 P Proline
20 4 11 Q Glutamine
20 2 12 H Histidine
49 6 13 A Alanine
43 10 13 E Glutamic acid
38 10 22 G Glycine
24 4 8 Y Tyrosine
28 5 17 V Valine
33 3 7 R Arginine
12 6 10 N Asparagine
30 8 9 I Isoleucine
9 4 2 M Methionine
22 2 12 F Phenylalanine 

6ILA_1|Chain A|Fructuronate-tagaturonate epimerase UxaE|Cohnella laeviribosi (380174)
>2MJD_1|Chain A|Adrenodoxin homolog, mitochondrial|Saccharomyces cerevisiae (559292)
>8BZZ_1|Chain A[auth AAA]|Carbonic anhydrase 2|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 \(w=f(c)\)
6ILA , Knot 193 489 0.81 40 241 461 
MKAQSIIERLAAGQVHVYPRSRHESEGTRVQMIKAEGRKYLVAEGSGKLYDELRGEEADGVKLCELSHENRLVLNRHFPFTVPQAFGKQSATIGLGDRLGIAGPGHVQTVRGRAIHPILAQQSIRELALTGRDYKQVIDAAAYAVFQEGYTEGYGADGDHLKKEEDIRMALDLGFTMLTLDCSEQIDNEAAQAGESEVKRKYEELPESVRSHYEAKYLDKTFQVGPHAIHFDAATLMRDVLVYREAIQFMIYIYEKYIQTAGRAVDFEISIDETLTPTAPGSHFLVASELIGKNVDIFSMAPRFIGEFQKGIDYIGDIAQFERELAVHAAIADRFGYKLSIHSGADKFSVFALVGRYTNGRFHVKTAGTNWLEAVRIVAKTNPGLYRRMHQYALEHFEEATAYYHVTTNLNNIRPLADVSDEELPSYMNENDARQLLHITYGLLLQAKKDDGSSLFRDEFFRTLSEREEDYEAALRSHIGKHLDLLGVK
2MJD , Knot 58 115 0.79 38 96 112 
GEELKITFILKDGSQKTYEVCEGETILDIAQGHNLDMEGACGGSCACSTCHVIVDPDYYDALPEPEDDENDMLDLAYGLTETSRLGCQIKMSKDIDGIRVALPQMTRNVNNNDFS
8BZZ , Knot 112 260 0.79 40 176 249 
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK

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 \(c\).

\(|P_{f(6ILA_1)}(2) \setminus P_{f(2MJD_1)}(2)|=172\), \(|P_{f(2MJD_1)}(2) \setminus P_{f(6ILA_1)}(2)|=27\). 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 1:101001100111101010100000001001011010100011101010100010100101101001000001110001110110111000101111001111111010010101101111000100111010000011011101110010001011010010000010111011101101000001000110110001000000110010000010010001011101101011011001110001101110100001001101101010100010101110011110011100101101110111010011001101101000111011110011001010011001011111100001010100110011011011100011100010001100100101000100010010111010000110010000100110100111101000010011000110010000000011100011001011110
Pair \(Z_2\) Length of longest common subsequence
6ILA_1,2MJD_1 199 4
6ILA_1,8BZZ_1 155 4
2MJD_1,8BZZ_1 180 3

Newick tree

 
[
	2MJD_1:99.99,
	[
		6ILA_1:77.5,8BZZ_1:77.5
	]:22.49
]

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 \((0.85)(0.8)(\frac{604 }{\log_{20} 604}-\frac{115}{\log_{20}115})=142.\)
Status Protein1 Protein2 d d1/2
Query variables 6ILA_1 2MJD_1 178 108
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]