CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4IWM_1 6IMH_1 6PRU_1 Letter Amino acid
28 0 3 K Lycine
8 0 6 T Threonine
13 0 14 A Alanine
2 0 12 R Arginine
18 0 10 D Aspartic acid
1 4 3 C Cysteine
13 0 4 H Histidine
22 0 9 I Isoleucine
16 2 7 G Glycine
2 0 1 M Methionine
15 1 6 S Serine
0 1 3 W Tryptophan
15 0 14 V Valine
2 0 11 Q Glutamine
34 2 16 L Leucine
13 0 6 F Phenylalanine
13 0 3 N Asparagine
21 1 14 E Glutamic acid
7 4 5 P Proline
9 1 3 Y Tyrosine 

4IWM_1|Chains A, B, C, D, E, F|UPF0135 protein MJ0927|Methanocaldococcus jannaschii (243232)
>6IMH_1|Chain A|(ACE)-GLY-CYS-PRO-CYS-GLU-PRO-SER-TYR-LEU-CYS-PRO-TRP-LEU-PRO-GLY-CYS-(NH2)|Enterobacteria phage M13 (1977402)
>6PRU_1|Chains A, B|Methyl-accepting chemotaxis protein|Thermosynechococcus elongatus (strain BP-1) (197221)
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 \(w=f(c)\)
4IWM , Knot 107 252 0.78 38 139 230 
MKAKEIIEFIETFAPKDLAIEGDNIGLQVGDNLDKEIKKLGIALDPSLSVIKKAEKEGVDFLFTHHPLLKDPIRNFTGVIYKKLKILMENDIILYSAHTNLDICKNGLNDALAELYNLENPKPLYDNGLGRVGIFKGSFEEFLEITKKYIHKNPIVVKSKEVDDNFKLAVLSGYGLSQSSIKYVAEKADVYLSGDLTHHSKILAEELGLVVVDATHYSTEVFGLKKFKEFLSSNLDLEIISLDFLEHHHHHH
6IMH , Knot 11 18 0.58 18 15 16 
XGCPCEPSYLCPWLPGCX
6PRU , Knot 72 150 0.80 40 115 146 
SELRDRQAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDIFKAGLTECHLNQLRPLKVRANLVVPMVIDDQLFGLLIAHQASEPRQWQEIEIDQFSELASTGSLVLERLH

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 \(c\).

\(|P_{f(4IWM_1)}(2) \setminus P_{f(6IMH_1)}(2)|=137\), \(|P_{f(6IMH_1)}(2) \setminus P_{f(4IWM_1)}(2)|=13\). 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 1:101001101100111001110100111011001000100111110101011001000110111000111001100101110001011100011100100010100011001110100100101100011101111010100110100001000111100001000101111010110000100110010101010100000111001111110100000011110010011000101011010110000000
Pair \(Z_2\) Length of longest common subsequence
4IWM_1,6IMH_1 150 2
4IWM_1,6PRU_1 154 3
6IMH_1,6PRU_1 126 2

Newick tree

 
[
	4IWM_1:79.87,
	[
		6IMH_1:63,6PRU_1:63
	]:16.87
]

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 \((0.85)(0.8)(\frac{270 }{\log_{20} 270}-\frac{18}{\log_{20}18})=85.5\)
Status Protein1 Protein2 d d1/2
Query variables 4IWM_1 6IMH_1 104 56
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]