CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6TSV_1 2LPJ_1 6CZF_1 Letter Amino acid
1 1 9 H Histidine
11 6 42 I Isoleucine
2 0 17 Y Tyrosine
17 17 47 A Alanine
6 1 39 R Arginine
9 3 36 D Aspartic acid
9 5 32 E Glutamic acid
17 11 34 G Glycine
0 0 7 C Cysteine
10 9 38 L Leucine
3 10 10 M Methionine
8 11 20 T Threonine
7 5 36 V Valine
3 10 30 N Asparagine
3 2 17 K Lycine
3 5 19 P Proline
12 22 23 S Serine
6 11 19 Q Glutamine
9 7 22 F Phenylalanine
1 1 1 W Tryptophan 

6TSV_1|Chains A, B, C, D|Tail tube protein Rcc01691|Rhodobacter capsulatus DE442 (1415160)
>2LPJ_1|Chain A|Major ampullate spidroin 1|Euprosthenops australis (332052)
>6CZF_1|Chains A, B, C, D|Amidophosphoribosyltransferase|Escherichia coli (strain K12) (83333)
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 \(w=f(c)\)
6TSV , Knot 67 137 0.80 38 109 133 
MAAQNGKDLLIKLDLTGSGQFETIAGLRATRISFNAETVDVTSLESQGGWRELLGGAGVRSASISGAGVFKDADTDERARQIFFDGEVPEFQVIIPDFGIVQGPFMITSIDYAGSHNGEASYELAMASAGALSFTAI
2LPJ , Knot 63 137 0.75 36 95 134 
GSGNSHTTPWTNPGLAENFMNSFMQGLSSMPGFTASQLDDMSTIAQSMVQSIQSLAAQGRTSPNKLQALNMAFASSMAEIAASEEGGGSLSTKTSSIASAMSNAFLQTTGVVNQPFINEITQLVSMFAQAGMNDVSA
6CZF , Knot 201 498 0.83 40 242 470 
CGIVGIAGVMPVNQSIYDALTVLQHRGQDAAGIITIDANNCFRLRKANGLVSDVFEARHMQRLQGNMGIGHVRYPTAGSSSASEAQPFYVNSPYGITLAHNGNLTNAHELRKKLFEEKRRHINTTSDSEILLNIFASELDNFRHYPLEADNIFAAIAATNRLIRGAYACVAMIIGHGMVAFRDPNGIRPLVLGKRDIDENRTEYMVASESVALDTLGFDFLRDVAPGEAIYITEEGQLFTRQCADNPVSNPCLFEYVYFARPDSFIDKISVYSARVNMGTKLGEKIAREWEDLDIDVVIPIPETSCDIALEIARILGKPYRQGFVKNRYVGRTFIMPGQQLRRKSVRRKLNANRAEFRDKNVLLVDDSIVRGTTSEQIIEMAREAGAKKVYLASAAPEIRFPNVYGIDMPSATELIAHGREVDEIRQIIGADGLIFQDLNDLIDAVRAENPDIQQFECSVFNGVYVTKDVDQGYLDFLDTLRNDDAKAVQRQNEVENL

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 \(c\).

\(|P_{f(6TSV_1)}(2) \setminus P_{f(2LPJ_1)}(2)|=73\), \(|P_{f(2LPJ_1)}(2) \setminus P_{f(6TSV_1)}(2)|=59\). 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 1:11100100111010101010100111101001010100101001000111001111111001010111110010000010011101011010111101111011111001001100010100011110111101011
Pair \(Z_2\) Length of longest common subsequence
6TSV_1,2LPJ_1 132 3
6TSV_1,6CZF_1 179 3
2LPJ_1,6CZF_1 191 3

Newick tree

 
[
	6CZF_1:99.84,
	[
		6TSV_1:66,2LPJ_1:66
	]:33.84
]

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 \((0.85)(0.8)(\frac{274 }{\log_{20} 274}-\frac{137}{\log_{20}137})=42.7\)
Status Protein1 Protein2 d d1/2
Query variables 6TSV_1 2LPJ_1 55 54
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]