CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9QPT_1 7OYH_1 2HWT_1 Letter Amino acid
47 34 9 E Glutamic acid
37 10 7 K Lycine
50 16 3 F Phenylalanine
95 35 2 V Valine
77 34 9 G Glycine
110 52 8 L Leucine
65 27 5 T Threonine
3 4 2 C Cysteine
48 25 4 P Proline
7 7 2 W Tryptophan
33 17 5 Y Tyrosine
116 54 6 A Alanine
32 49 6 R Arginine
49 19 3 N Asparagine
36 40 2 D Aspartic acid
78 20 5 S Serine
54 20 5 Q Glutamine
12 14 3 H Histidine
66 18 4 I Isoleucine
40 13 4 M Methionine 

9QPT_1|Chains A, B, C|Multidrug resistance protein MdtF|Escherichia coli K-12 (83333)
>7OYH_1|Chain A|Depupylase|Acidothermus cellulolyticus (28049)
>2HWT_1|Chain A|Putative replicase-associated protein|Faba bean necrotic yellows virus (59817)
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 \(w=f(c)\)
9QPT , Knot 380 1055 0.83 40 295 929 
MANYFIDRPVFAWVLAIIMMLAGGLAIMNLPVAQYPQIAPPTITVSATYPGADAQTVEDSVTQVIEQNMNGLDGLMYMSSTSDAAGNASITLTFETGTSPDIAQVQVQNKLQLAMPSLPEAVQQQGISVDKSSSNILMVAAFISDNGSLNQYDIADYVASNIKDPLSRTAGVGSVQLFGSEYAMRIWLDPQKLNKYNLVPSDVISQIKVQNNQISGGQLGGMPQAADQQLNASIIVQTRLQTPEEFGKILLKVQQDGSQVLLRDVARVELGAEDYSTVARYNGKPAAGIAIKLAAGANALDTSRAVKEELNRLSAYFPASLKTVYPYDTTPFIEISIQEVFKTLVEAIILVFLVMYLFLQNFRATIIPTIAVPVVILGTFAILSAVGFTINTLTMFGMVLAIGLLVDDAIVVVENVERVIAEDKLPPKEATHKSMGQIQRALVGIAVVLSAVFMPMAFMSGATGEIYRQFSITLISSMLLSVFVAMSLTPALCATILKAAPEGGHKPNALFARFNTLFEKSTQHYTDSTRSLLRCTGRYMVVYLLICAGMAVLFLRTPTSFLPEEDQGVFMTTAQLPSGATMVNTTKVLQQVTDYYLTKEKDNVQSVFTFGGFGFSGQGQNNGLAFISLKPWSERVGEENSVTAIIQRAMIALSSINKAVVFPFNLPAVAELGTASGFDMELLDNGNLGHEKLTQARNELLSLAAQSPNQVTGVRPNGLEDTPMFKVNVNAAKAEAMGVALSDINQTISTAFGSSYVNDFLNQGRVKKVYVQAGTPFRMLPDNINQWYVRNASGTMAPLSAYSSTEWTYGSPRLERYNGIPSMEILGEAAAGKSTGDAMKFMADLVAKLPAGVGYSWTGLSYQEALSSNQAPALYAISLVVVFLALAALYESWSIPFSVMLVVPLGVVGALLATDLRGLSNDVYFQVGLLTTIGLSAKNAILIVEFAVEMMQKEGKTPIEAIIEAARMRLRPILMTSLAFILGVLPLVISHGAGSGAQNAVGTGVMGGMFAATVLAIYFVPVFFVVVEHLFARFKKAASGENLYFQSLEHHHHHH
7OYH , Knot 205 508 0.83 40 239 476 
MHRVMGIETEYGISVPHQPNANAMAASSQVVNAYAPIGAPAQRQARWDFEEENPLRDARGFEVAREAADPSQLTDEDLGLANVILTNGARLYVDHAHPEYSTPEVTNPRDAVLWDKAGERIMAEAARRAADLPMGWTIQLYKNNTDNKGASYGCHENYLMNRSTPFADIVRHLIPFFVTRQVFCGAGRVGIGADGRGEGFQLSQRADFFEVEVGLETTLKRPIINTRDEPHADPEKYRRLHVIIGDANMSEIATYLKLGTTALVLAMIEDGFLSQDFSVESPVGALRAVSHDPTLRYQLRLHDGRRLTAVQLQMEYLEQARKYVEDRFGTDVDDMTRDVLDRWETTLVRLADDPMQLSRDLDWVAKLSILEGYRQRENLPWSAHKLQLVDLQYHDVRPDRGLYNRLVARGRMNLLVDEAAVRTAMHEPPNDTRAYFRGRCLAKFGAEIAAASWDSVIFDLPGRDSLQRVPTLEPLRGTRAHVGDLLDRCRSATELVAALTGGENLYFQ
2HWT , Knot 48 94 0.77 40 76 87 
ARQVICWCFTLNNPLSPLSLHDSMKYLVYQTEQGEAGNIHFQGYIEMKKRTSLAGMKKLIPGAHFEKRRGTQGEARAYSMKEDTRLEGPWEYGE

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 \(c\).

\(|P_{f(9QPT_1)}(2) \setminus P_{f(7OYH_1)}(2)|=94\), \(|P_{f(7OYH_1)}(2) \setminus P_{f(9QPT_1)}(2)|=38\). 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 1:11001100111111111111111111110111100101111010101001110100100010011000101101110100000111010101010010010110101000101111011011000110100000011111111000101000011001100100110001111010111000110111010010000111001100101000010110111110110001010111000100100110111010001001110011010111000001100010111111101111101100001100010010101110100101000011101010011001101111111110111001010111011111111101111011110100101111111111110011111001001110001110010000110100111111111011111111101101010001010110011101111101011101011011101100101111010011000000000000011000100111011101111111100100111000011110010110110110000110010000100000010011011111101010001111101011000110000101110011111001001111110111110110101101011001011000100100011011100100101101011000111010101101011111100100010011100010011001010010101101101110010010100101011110100000100101010000111010111011110001011011101110111111001011000011000011110110111111111110001011101111111111111110010110001010111100111010011111011101100010011011101101010111100111111111111001110110011101111111110111101111111110011101001101001010010000000
Pair \(Z_2\) Length of longest common subsequence
9QPT_1,7OYH_1 132 7
9QPT_1,2HWT_1 247 4
7OYH_1,2HWT_1 209 3

Newick tree

 
[
	2HWT_1:12.47,
	[
		9QPT_1:66,7OYH_1:66
	]:60.47
]

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 \((0.85)(0.8)(\frac{1563 }{\log_{20} 1563}-\frac{508}{\log_{20}508})=266.\)
Status Protein1 Protein2 d d1/2
Query variables 9QPT_1 7OYH_1 330 244
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]