CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4ODX_1 3LHQ_1 7AEW_1 Letter Amino acid
9 20 24 A Alanine
7 9 5 F Phenylalanine
10 6 5 P Proline
7 15 13 R Arginine
0 4 2 C Cysteine
8 12 7 Q Glutamine
14 15 10 I Isoleucine
10 28 24 L Leucine
3 10 17 K Lycine
7 16 19 S Serine
3 3 2 W Tryptophan
9 8 7 N Asparagine
13 6 14 D Aspartic acid
4 5 10 Y Tyrosine
18 12 12 V Valine
11 5 3 H Histidine
6 7 9 M Methionine
5 11 10 T Threonine
9 21 29 E Glutamic acid
8 7 14 G Glycine 

4ODX_1|Chains A[auth X], F[auth Y]|4E10 epitope scaffold T117|artificial gene (32630)
>3LHQ_1|Chains A, B|AcrAB operon repressor (TetR/AcrR family)|Salmonella enterica subsp. enterica serovar Typhimurium (99287)
>7AEW_1|Chain A[auth AAA]|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 \(w=f(c)\)
4ODX , Knot 78 161 0.82 38 120 154 
HHHHHHNAMQGIHFRRHYVRHLPKEVSQNDIIKALASPLINDGMVVSDFADHVITREQNFPTGLPVEPVGVAIPHTDSKYVRQNAISVGILAEPVNFEDAGGEPDPVPVRVVFMLALGNWFDITNVLWWIMDVIQDEDFMQQLLVMNDDEIYQSIYTRISE
3LHQ , Knot 103 220 0.84 40 154 214 
SNAMARKTKQQALETRQHILDVALRLFSQQGVSATSLAEIANAAGVTRGAIYWHFKNKSDLFSEIWELSESNIGELEIEYQAKFPDDPLSVLREILVHILEATVTEERRRLLMEIIFHKCEFVGEMVVVQQAQRSLCLESYDRIEQTLKHCINAKMLPENLLTRRAAILMRSFISGLMENWLFAPQSFDLKKEARAYVTILLEMYQLCPTLRASTVNGSP
7AEW , Knot 108 236 0.83 40 164 229 
GAMGSMERASLIQKAKLAEQAERYEDMAAFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEGSEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWT

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 \(c\).

\(|P_{f(4ODX_1)}(2) \setminus P_{f(3LHQ_1)}(2)|=63\), \(|P_{f(3LHQ_1)}(2) \setminus P_{f(4ODX_1)}(2)|=97\). 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 1:00000001101101000010011001000011011101110011110011001100000110111101111111000000100011011111011010011101011110111111110110100111111011000011001111000010001000100
Pair \(Z_2\) Length of longest common subsequence
4ODX_1,3LHQ_1 160 3
4ODX_1,7AEW_1 160 3
3LHQ_1,7AEW_1 158 4

Newick tree

 
[
	4ODX_1:80.33,
	[
		3LHQ_1:79,7AEW_1:79
	]:1.33
]

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 \((0.85)(0.8)(\frac{381 }{\log_{20} 381}-\frac{161}{\log_{20}161})=66.0\)
Status Protein1 Protein2 d d1/2
Query variables 4ODX_1 3LHQ_1 85 73.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]