CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8ALV_1 3VBD_1 8WEQ_1 Letter Amino acid
9 1 6 M Methionine
2 7 9 W Tryptophan
14 19 32 D Aspartic acid
7 11 14 Q Glutamine
3 12 14 H Histidine
2 1 1 C Cysteine
24 26 34 L Leucine
5 12 21 F Phenylalanine
10 12 19 T Threonine
10 8 12 Y Tyrosine
24 13 36 A Alanine
29 13 23 E Glutamic acid
10 9 17 I Isoleucine
17 24 12 K Lycine
5 17 13 P Proline
19 18 31 S Serine
12 17 27 V Valine
13 7 28 R Arginine
7 10 12 N Asparagine
14 22 35 G Glycine 

8ALV_1|Chain A|14-3-3 protein sigma|Homo sapiens (9606)
>3VBD_1|Chain A|Carbonic anhydrase 2|Homo sapiens (9606)
>8WEQ_1|Chains A, B, C, D|4-hydroxybenzoate 3-monooxygenase|Arthrobacter sp. PAMC25564 (2565366)
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 \(w=f(c)\)
8ALV , Knot 108 236 0.83 40 164 229 
GAMGSMERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWT
3VBD , Knot 111 259 0.79 40 175 248 
SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
8WEQ , Knot 169 396 0.85 40 217 378 
MANRKVITTQVAIMGAGPAGLMLSHLLAKAGIESTVIEIRSHQEISETVRAGILEHGSVNLLVDSGASDRVLRDGDRHDGIELRFNGESHRIDFQDLVGESVWLYPQTDVFLDLAARRQADGGDVRYSVTDTTIHDLEGKPKVWFTDADGVEYELQADFIAGADGSRSHSRFQIPEAQRKWYFHEYPFAWFGILAETPRSSDELIYANSENGFALISQRTETVQRLYFQCDPNEDVNDWSDDRIWDAFRSRVNGNGFELKEGPVIDKTVLKFRSFVHAPMRHGNLFLAGDAAHTVPPTGAKGLNLALHDVKVLFEGFDSFYKSGSTALLDGYSGRALDRVWKAQQFSYWMTSMLHTPVGGDDFARARQLGELNSVVSSRHGRAYLAEAYTGWPASS

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 \(c\).

\(|P_{f(8ALV_1)}(2) \setminus P_{f(3VBD_1)}(2)|=76\), \(|P_{f(3VBD_1)}(2) \setminus P_{f(8ALV_1)}(2)|=87\). 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 1:11110100101100101100100000111110111001001000000110110001111001110110010000000100001101000000100010110001111100011001101000110101010000011011010000011001001000110100001110011011111010110001100100110110001001110100100000000011101100010110
Pair \(Z_2\) Length of longest common subsequence
8ALV_1,3VBD_1 163 3
8ALV_1,8WEQ_1 167 4
3VBD_1,8WEQ_1 182 5

Newick tree

 
[
	8WEQ_1:89.18,
	[
		8ALV_1:81.5,3VBD_1:81.5
	]:7.68
]

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 \((0.85)(0.8)(\frac{495 }{\log_{20} 495}-\frac{236}{\log_{20}236})=74.5\)
Status Protein1 Protein2 d d1/2
Query variables 8ALV_1 3VBD_1 94 90.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]