CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6GQW_1 7CTZ_1 2CAG_1 Letter Amino acid
3 17 2 C Cysteine
5 12 19 H Histidine
8 26 24 S Serine
12 26 20 T Threonine
10 18 32 R Arginine
15 41 36 D Aspartic acid
9 19 18 Q Glutamine
11 49 20 I Isoleucine
4 17 14 M Methionine
7 34 32 F Phenylalanine
4 19 29 P Proline
0 6 7 W Tryptophan
9 13 35 A Alanine
4 63 24 N Asparagine
9 38 18 Y Tyrosine
11 50 31 L Leucine
15 35 26 V Valine
11 61 29 K Lycine
12 39 34 E Glutamic acid
12 25 34 G Glycine 

6GQW_1|Chains A, B, C, D, F|GTPase KRas|Homo sapiens (9606)
>7CTZ_1|Chains A, B|Bifunctional dihydrofolate reductase-thymidylate synthase|Plasmodium falciparum (5833)
>2CAG_1|Chain A|CATALASE COMPOUND II|Proteus mirabilis (584)
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 \(w=f(c)\)
6GQW , Knot 83 171 0.83 38 134 169 
YFQGMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGHEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHK
7CTZ , Knot 239 608 0.84 40 265 548 
MMEQVCDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCNSLDMKYFCAVTTYVNESKYEKLKYKRCKYLNKETVDNVNDMPNSKKLQNVVVMGRTSWESIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFIIGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFIIYKKTNNKMLNEQNCIKGEEKNNDMPLKNDDKDTCHMKKLTEFYKNVDKYKINYENDDDDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA
2CAG , Knot 201 484 0.85 40 259 461 
MEKKKLTTAAGAPVVDNNNVITAGPRGPMLLQDVWFLEKLAHFDREVIPERRMHAKGSGAFGTFTVTHDITKYTRAKIFSEVGKKTEMFARFSTVAGERGAADAERDIRGFALKFYTEEGNWDMVGNNTPVFYLRDPLKFPDLNHIVKRDPRTNMRNMAYKWDFFSHLPESLHQLTIDMSDRGLPLSYRFVHGFGSHTYSFINKDNERFWVKFHFRCQQGIKNLMDDEAEALVGKDRESSQRDLFEAIERGDYPRWKLQIQIMPEKEASTVPYNPFDLTKVWPHADYPLMDVGYFELNRNPDNYFSDVEQAAFSPANIVPGISFSPDKMLQGRLFSYGDAHRYRLGVNHHQIPVNAPKCPFHNYHRDGAMRVDGNSGNGITYEPNSGGVFQEQPDFKEPPLSIEGAADHWNHREDEDYFSQPRALYELLSDDEHQRMFARIAGELSQASKETQQRQIDLFTKVHPEYGAGVEKAIKVLEGKDAK

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 \(c\).

\(|P_{f(6GQW_1)}(2) \setminus P_{f(7CTZ_1)}(2)|=35\), \(|P_{f(7CTZ_1)}(2) \setminus P_{f(6GQW_1)}(2)|=166\). 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 1:010110000111111111100110101100011000010100000001110100011011001100000110000100101110111100000100100000010010000011111110000110001000010011000111110001000011001100110010000
Pair \(Z_2\) Length of longest common subsequence
6GQW_1,7CTZ_1 201 3
6GQW_1,2CAG_1 201 3
7CTZ_1,2CAG_1 160 4

Newick tree

 
[
	6GQW_1:10.45,
	[
		7CTZ_1:80,2CAG_1:80
	]:26.45
]

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 \((0.85)(0.8)(\frac{779 }{\log_{20} 779}-\frac{171}{\log_{20}171})=170.\)
Status Protein1 Protein2 d d1/2
Query variables 6GQW_1 7CTZ_1 216 138.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]