CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7GHO_1 1LSX_1 3DGZ_1 Letter Amino acid
17 5 13 F Phenylalanine
13 6 23 P Proline
9 9 30 E Glutamic acid
29 10 42 L Leucine
11 1 31 K Lycine
11 3 14 Y Tyrosine
14 8 24 Q Glutamine
26 12 52 G Glycine
17 7 18 D Aspartic acid
7 7 19 H Histidine
11 14 22 I Isoleucine
10 5 11 M Methionine
16 9 26 S Serine
17 5 40 A Alanine
11 12 16 R Arginine
24 11 35 T Threonine
3 1 7 W Tryptophan
27 4 44 V Valine
21 2 11 N Asparagine
12 0 10 C Cysteine 

7GHO_1|Chains A, B|3C-like proteinase|Severe acute respiratory syndrome coronavirus 2 (2697049)
>1LSX_1|Chain A|Sensor protein FixL|Bradyrhizobium japonicum (375)
>3DGZ_1|Chain A|Thioredoxin reductase 2|Mus musculus (10090)
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 \(w=f(c)\)
7GHO , Knot 134 306 0.83 40 196 290 
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ
1LSX , Knot 67 131 0.83 38 108 129 
MRETHLRSILHTIPDAMIVIDGHGIIQLFSTAAERLFGWSELEAIGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQSGGEPYFTGFVRDLTEHQQTQARLQELQ
3DGZ , Knot 202 488 0.85 40 252 465 
AGGQQSFDLLVIGGGSGGLACAKEAAQLGKKVAVADYVEPSPRGTKWGLGGTCVNVGCIPKKLMHQAALLGGMIRDAHHYGWEVAQPVQHNWKTMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVRGVDKGGKATLLSAEHIVIATGGRPRYPTQVKGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTVMMRSIPLRGFDQQMSSLVTEHMESHGTQFLKGCVPSHIKKLPTNQLQVTWEDHASGKEDTGTFDTVLWAIGRVPETRTLNLEKAGISTNPKNQKIIVDAQEATSVPHIYAIGDVAEGRPELTPTAIKAGKLLAQRLFGKSSTLMDYSNVPTTVFTPLEYGCVGLSEEEAVALHGQEHVEVYHAYYKPLEFTVADRDASQCYIKMVCMREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMQTVGIHPTCSEEVVKLHISKRSGLEPTVTG

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 \(c\).

\(|P_{f(7GHO_1)}(2) \setminus P_{f(1LSX_1)}(2)|=145\), \(|P_{f(1LSX_1)}(2) \setminus P_{f(7GHO_1)}(2)|=57\). 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 1:011001111010101011010010001011110011001001100000110100001110000001110110101011100100011010100101001000110101100101110001010110001101010101011010010111010000101001001011011011001010101111000010111000010101111101111010011100100010010111100000110000101111101001111101010100110011010011101110001011011000011010
Pair \(Z_2\) Length of longest common subsequence
7GHO_1,1LSX_1 202 3
7GHO_1,3DGZ_1 164 3
1LSX_1,3DGZ_1 196 4

Newick tree

 
[
	1LSX_1:10.69,
	[
		7GHO_1:82,3DGZ_1:82
	]:22.69
]

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 \((0.85)(0.8)(\frac{437 }{\log_{20} 437}-\frac{131}{\log_{20}131})=91.6\)
Status Protein1 Protein2 d d1/2
Query variables 7GHO_1 1LSX_1 120 85.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]