CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4LUU_1 6JHX_1 7HQI_1 Letter Amino acid
24 37 9 D Aspartic acid
38 25 19 L Leucine
20 22 6 T Threonine
12 16 0 W Tryptophan
21 15 11 S Serine
33 25 2 R Arginine
29 26 6 E Glutamic acid
7 43 13 K Lycine
6 16 2 M Methionine
15 29 5 F Phenylalanine
9 26 16 N Asparagine
12 23 6 I Isoleucine
14 24 7 Y Tyrosine
20 28 5 P Proline
23 34 22 V Valine
41 34 15 A Alanine
4 0 3 C Cysteine
4 25 3 Q Glutamine
24 36 13 G Glycine
26 8 6 H Histidine 

4LUU_1|Chain A|Epi-isozizaene synthase|Streptomyces coelicolor (100226)
>6JHX_1|Chains A, B|AlgQ2|Sphingomonas sp (28214)
>7HQI_1|Chains A, B|Non-structural protein 3|Severe acute respiratory syndrome coronavirus 2 (2697049)
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 \(w=f(c)\)
4LUU , Knot 157 382 0.81 40 201 354 
MGSSHHHHHHSSGLVPRGSHMVHAFPHGTTATPTAIAVPPSLRLPVIEAAFPRQLHPYWPKLQETTRTWLLEKRLMPADKVEEYADGLCYTDLMAGYYLGAPDEVLQAIADYSAWFFVWDDRHDRDIVHGRAGAWRRLRGLLHTALDSPGDHLHHEDTLVAGFADSVRRLYAFLPATWNARFARHFHTVIEAYDREFHNRTRGIVPGVEEYLELRRLTFAHWIWTDLLEPSSGCELPDAVRKHPAYRRAALLSQEFAAWYNDLCSLPKEIAGDEVHNLGISLITHHSLTLEEAIGEVRRRVEECITEFLAVERDALRFADELADGTVRGKELSGAVRANVGNMRNWFSSAYWFHHESGRYMVDSWDDRSTPPYVNNEAAGEK
6JHX , Knot 200 492 0.84 38 254 467 
KEATWVTDKPLTLKIHMHFRDKWVWDENWPVAKESFRLTNVKLQSVANKAATNSQEQFNLMMASGDLPDVVGGDNLKDKFIQYGQEGAFVPLNKLIDQYAPHIKAFFKSHPEVERAIKAPDGNIYFIPYVPDGVVARGYFIREDWLKKLNLKPPQNIDELYTVLKAFKEKDPNGNGKAAAVPFIDRHPDEVFRLVNFWGARSSGSDNYMDFYIDNGRVKHPWAETAFRDGMKHVAQWYKEGLIDKEIFTRKARAREQMFGGNLGGFTHDWFASTMTFNEGLAKTVPGFKLIPIAPPTNSKGQRWEEDSRQKVRPDGWAITVKNKNPVETIKFFDFYFSRPGRDISNFGVPGVTYDIKNGKAVFKDSVLKSPQPVNNQLYDMGAQIPIGFWQDYDYERQWTTPEAQAGIDMYVKGKYVMPGFEGVNMTREERAIYDKYWADVRTYMYEMGQAWVMGTKDVDKTWDEYQRQLKLRGLYQVLQMMQQAYDRQYKN
7HQI , Knot 80 169 0.81 38 119 162 
SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFL

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 \(c\).

\(|P_{f(4LUU_1)}(2) \setminus P_{f(6JHX_1)}(2)|=64\), \(|P_{f(6JHX_1)}(2) \setminus P_{f(4LUU_1)}(2)|=117\). 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 1:1100000000001111010011011101001010111111010111101111001010110100000011100011110010001011000011110011110011011100011111100000001101011110010111001100110010000011111100100101111101010110010011010000100000111111000101001011011100110100100110110001100011110001111000100110011100100111011000010100111010001000100111100011011001101010100101110101101001100101100001001100100000110100011100
Pair \(Z_2\) Length of longest common subsequence
4LUU_1,6JHX_1 181 4
4LUU_1,7HQI_1 184 3
6JHX_1,7HQI_1 195 3

Newick tree

 
[
	7HQI_1:96.17,
	[
		4LUU_1:90.5,6JHX_1:90.5
	]:5.67
]

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 \((0.85)(0.8)(\frac{874 }{\log_{20} 874}-\frac{382}{\log_{20}382})=131.\)
Status Protein1 Protein2 d d1/2
Query variables 4LUU_1 6JHX_1 174 152
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]