CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9EIF_1 6UYE_1 2EQL_1 Letter Amino acid
6 13 13 N Asparagine
11 4 2 H Histidine
5 0 4 M Methionine
9 11 4 Y Tyrosine
25 13 4 R Arginine
37 15 1 P Proline
3 5 5 W Tryptophan
45 20 5 V Valine
15 13 15 K Lycine
14 19 13 S Serine
28 21 1 T Threonine
21 12 10 D Aspartic acid
9 7 2 Q Glutamine
32 22 7 G Glycine
48 21 10 L Leucine
12 15 5 F Phenylalanine
45 16 11 A Alanine
7 5 8 C Cysteine
32 18 6 E Glutamic acid
21 11 3 I Isoleucine 

9EIF_1|Chains A, B|A broad-substrate spectrum lactate racemase A|Isosphaera pallida (128)
>6UYE_1|Chains A, E[auth B], I[auth C]|SGP|Ebola virus (1570291)
>2EQL_1|Chain A|HORSE MILK LYSOZYME|Equus caballus (9796)
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 \(w=f(c)\)
9EIF , Knot 170 425 0.80 40 208 389 
RVTLDYGKTGLNVDLPDDRTLPPLTIRPAPPLDDPEAEVVRCLAEPIGSPPLLDLARGKRSACILVCDITRPVPNPVLLRPILRTLHAAGLATQDILILVATGLHRPSTPAEKVEMLSEEIARTYRVEDHYGTRLEEHTYLGTTPNGVPAWIDSRYVQADLKIATGLIEPHLMAGYSGGRKLICPGIAAFETVKLWHGPRFLEHPLADCGFLEGNPVHEENTRIARMAGCDFIVNVTLDGARRITSVVAGDMEQAFLKGVAFVETVVKAAVPAPVDVVVTSSAGHPLDLTFYQAVKGLTGALPIVKPGGTIVIAAALAEGLGSPEFQSLFEEHPTLEGFMEAILKEESFTVDQWQLEELAKVRRKARVKFVSDGVPAAVLSRCHVEPVATVELAVAQALEQYGPEARVAVIPKGPYVLPVVDPTL
6UYE , Knot 116 261 0.82 38 171 252 
SIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSVTKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYASGKRSNTTGKLIWKVNPEIDTTIGEWAFWE
2EQL , Knot 67 129 0.84 40 104 126 
KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDPKGMSAWKAWVKHCKDKDLSEYLASCNL

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 \(c\).

\(|P_{f(9EIF_1)}(2) \setminus P_{f(6UYE_1)}(2)|=97\), \(|P_{f(6UYE_1)}(2) \setminus P_{f(9EIF_1)}(2)|=60\). 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 1:01010010011010110000111101011111001010110011011101111011010001011100100111011110111001011111000111111011001001100101100011000010000100100000110010111111000010101011011101011110011001101111110010110110110011100111010110000001101110011101010110010011110100111011111001101111111011100011011010100110110111111011101111111101110101001100010101110111000010100101001101000101011001111111000010111010111101100011010111110110111110101
Pair \(Z_2\) Length of longest common subsequence
9EIF_1,6UYE_1 157 4
9EIF_1,2EQL_1 200 3
6UYE_1,2EQL_1 179 3

Newick tree

 
[
	2EQL_1:99.76,
	[
		9EIF_1:78.5,6UYE_1:78.5
	]:21.26
]

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 \((0.85)(0.8)(\frac{686 }{\log_{20} 686}-\frac{261}{\log_{20}261})=118.\)
Status Protein1 Protein2 d d1/2
Query variables 9EIF_1 6UYE_1 146 116.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]