CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
1BMK_1 6LRE_1 1RSU_1 Letter Amino acid
20 20 4 R Arginine
18 12 2 P Proline
26 16 18 A Alanine
27 19 4 D Aspartic acid
15 12 3 Q Glutamine
18 14 16 G Glycine
19 43 4 K Lycine
25 28 11 S Serine
18 14 19 T Threonine
23 18 7 V Valine
4 10 0 C Cysteine
23 32 5 E Glutamic acid
22 18 3 I Isoleucine
43 41 7 L Leucine
11 5 1 M Methionine
13 23 2 F Phenylalanine
15 11 6 Y Tyrosine
14 18 7 N Asparagine
20 8 2 H Histidine
5 4 6 W Tryptophan 

1BMK_1|Chain A|PROTEIN (MAP KINASE P38)|Homo sapiens (9606)
>6LRE_1|Chains A, B|Cyclic GMP-AMP synthase|Homo sapiens (9606)
>1RSU_1|Chain A[auth B]|STREPTAVIDIN|Streptomyces avidinii (1895)
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 \(w=f(c)\)
1BMK , Knot 166 379 0.86 40 227 363 
GSSHHHHHHSSGLVPRGSHMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGHRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLAQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
6LRE , Knot 151 366 0.81 40 206 349 
DAAPGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
1RSU , Knot 60 127 0.76 38 89 121 
MEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAAS

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 \(c\).

\(|P_{f(1BMK_1)}(2) \setminus P_{f(6LRE_1)}(2)|=95\), \(|P_{f(6LRE_1)}(2) \setminus P_{f(1BMK_1)}(2)|=74\). 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 1:1000000000011110100100001010000100011011000001011101101010111000010011100100110011010000001011001000011111011011001001001011001111010011000010000101110011011001001011000101001110000010110111100000010101100100110111011000001011011011101101001111000100101110111011101100100001000100110110101101111101111011001111000001011011101011000010001110100001000011100100100001101111110000100
Pair \(Z_2\) Length of longest common subsequence
1BMK_1,6LRE_1 169 4
1BMK_1,1RSU_1 190 4
6LRE_1,1RSU_1 197 3

Newick tree

 
[
	1RSU_1:10.52,
	[
		1BMK_1:84.5,6LRE_1:84.5
	]:16.02
]

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 \((0.85)(0.8)(\frac{745 }{\log_{20} 745}-\frac{366}{\log_{20}366})=103.\)
Status Protein1 Protein2 d d1/2
Query variables 1BMK_1 6LRE_1 131 128.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]