CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1BLP_1 1NZY_1 7NLA_1 Letter Amino acid
16 23 12 V Valine
0 5 2 C Cysteine
22 19 24 L Leucine
9 11 7 P Proline
13 12 10 T Threonine
13 5 10 Y Tyrosine
0 6 2 W Tryptophan
18 36 27 A Alanine
4 20 13 R Arginine
12 19 17 G Glycine
43 10 17 K Lycine
19 9 20 S Serine
17 14 15 D Aspartic acid
4 6 9 Q Glutamine
3 11 9 M Methionine
7 9 5 F Phenylalanine
22 6 8 N Asparagine
14 20 33 E Glutamic acid
2 11 3 H Histidine
19 17 10 I Isoleucine 

1BLP_1|Chain A|BETA-LACTAMASE|Staphylococcus aureus (1280)
>1NZY_1|Chains A, C|4-CHLOROBENZOYL COENZYME A DEHALOGENASE|Pseudomonas sp. (72586)
>7NLA_1|Chain A|14-3-3 protein sigma|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 \(w=f(c)\)
1BLP , Knot 111 257 0.80 36 141 239 
KELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDITLKALIEASMTYSDNTANNKIIKEIGGIKKVKQRLKELGDKVTNPVRYEIELNYYSPKSKKNTSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF
1NZY , Knot 124 269 0.86 40 175 261 
MYEAIGHRVEDGVAEITIKLPRHRNALSVKAMQEVTDALNRAEEDDSVGAVMITGAEDAFCAGFYLREIPLDKGVAGVRDHFRIAALWWHQMIHKIIRVKRPVLAAINGVAAGGGLGISLASDMAICADSAKFVCAWHTIGIGNDTATSYSLARIVGMRRAMELMLTNRTLYPEEAKDWGLVSRVYPKDEFREVAWKVARELAAAPTHLQVMAKERFHAGWMQPVEECTEFEIQNVIASVTHPHFMPCLTRFLDGHRADRPQVELPAGV
7NLA , Knot 114 253 0.83 40 170 244 
GAMGSMERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEEGGEAPQEPQS

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 \(c\).

\(|P_{f(1BLP_1)}(2) \setminus P_{f(1NZY_1)}(2)|=67\), \(|P_{f(1NZY_1)}(2) \setminus P_{f(1BLP_1)}(2)|=101\). 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 1:00100100000101110110000100101000001101000011001111001100010001010000111001110001100101011101010000001000110011110010001001100100110001010000100000000111110010011101010000001110111000010011001110000110001011001000011110101000111111100000000010001100010011001
Pair \(Z_2\) Length of longest common subsequence
1BLP_1,1NZY_1 168 4
1BLP_1,7NLA_1 151 3
1NZY_1,7NLA_1 157 4

Newick tree

 
[
	1NZY_1:83.13,
	[
		1BLP_1:75.5,7NLA_1:75.5
	]:7.63
]

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 \((0.85)(0.8)(\frac{526 }{\log_{20} 526}-\frac{257}{\log_{20}257})=76.6\)
Status Protein1 Protein2 d d1/2
Query variables 1BLP_1 1NZY_1 102 94.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]