CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6DHA_1 5QQX_1 9LVA_1 Letter Amino acid
13 19 29 T Threonine
8 24 12 R Arginine
1 10 9 C Cysteine
19 25 13 E Glutamic acid
21 22 32 I Isoleucine
9 15 13 M Methionine
15 22 36 F Phenylalanine
16 37 34 S Serine
24 21 20 K Lycine
0 4 17 W Tryptophan
16 36 52 A Alanine
18 23 18 D Aspartic acid
16 19 13 Q Glutamine
6 26 26 H Histidine
38 45 49 L Leucine
10 21 17 P Proline
14 33 38 V Valine
8 15 20 N Asparagine
11 37 38 G Glycine
8 15 24 Y Tyrosine 

6DHA_1|Chains A, B|Peroxisome proliferator-activated receptor gamma|Homo sapiens (9606)
>5QQX_1|Chains A, B|5-aminolevulinate synthase, erythroid-specific, mitochondrial|Homo sapiens (9606)
>9LVA_1|Chain A|Auxin transporter protein 1|Arabidopsis thaliana (3702)
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 \(w=f(c)\)
6DHA , Knot 120 271 0.82 38 172 260 
ESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
5QQX , Knot 196 469 0.85 40 260 444 
MGHHHHHHSSGVDLGTENLYFQSMFSYDQFFRDKIMEKKQDHTYRVFKTVNRWADAYPFAQHFSEASVASKDVSVWCSNDYLGMSRHPQVLQATQETLQRHGVGAGGTRNISGTSKFHVELEQELAELHQKDSALLFSSCFVANDSTLFTLAKILPGCEIYSDAGNHASMIQGIRNSGAAKFVFRHNDPDHLKKLLEKSNPKIPKIVAFETVHSMDGAICPLEELCDVSHQYGALTFVDEVHAVGLYGSRGAGIGERDGIMHKIDIISGTLGKAFGCVGGYIASTRDLVDMVRSYAAGFIFTTSLPPMVLSGALESVRLLKGEEGQALRRAHQRNVKHMRQLLMDRGLPVIPCPSHIIPIRVGNAALNSKLCDLLLSKHGIYVQAINYPTVPRGEELLRLAPSPHHSPQMMEDFVEKLLLAWTAVGLPLQDVSVAACNFCRRPVHFELMSEWERSYFGNMGPQYVTTYA
9LVA , Knot 203 510 0.82 40 245 469 
MHHHHHHHHHHGSVEDYKDDDDKGSMSEGVEAIVANDNGTDQVNGNRTGKDNEEHDGSTGSNLSNFLWHGGSVWDAWFSCASNQVAQVLLTLPYSFSQLGMLSGIVLQIFYGLLGSWTAYLISVLYVEYRARKEKEGKSFKNHVIQWFEVLDGLLGSYWKALGLAFNCTFLLFGSVIQLIACASNIYYINDHLDKRTWTYIFGACCATTVFIPSFHNYRIWSFLGLGMTTYTAWYLAIASIIHGQAEGVKHSGPTKLVLYFTGATNILYTFGGHAVTVEIMHAMWKPQKFKYIYLMATLYVFTLTIPSAAAVYWAFGDALLDHSNAFSLMPKNAWRDAAVILMLIHQFITFGFACTPLYFVWEKVIGMHDTKSICLRALARLPVVIPIWFLAIIFPFFGPINSAVGALLVSFTVYIIPSLAHMLTYRSASARQNAAEKPPFFMPSWTAMYVLNAFVVVWVLIVGFGFGGWASVTNFVRQVDTFGLFAKCYQCKPAAAAAHAPVSALHHRL

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 \(c\).

\(|P_{f(6DHA_1)}(2) \setminus P_{f(5QQX_1)}(2)|=42\), \(|P_{f(5QQX_1)}(2) \setminus P_{f(6DHA_1)}(2)|=130\). 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 1:0010101110010000100111001010111010000001111001001111000101001011000000111011010010010110010001001111101010001011001100110011101100011110010111000110010011101101010111010110100001111111111010011110101100100011011010101001000011101100100100110001011011000000101011100100010
Pair \(Z_2\) Length of longest common subsequence
6DHA_1,5QQX_1 172 3
6DHA_1,9LVA_1 183 5
5QQX_1,9LVA_1 175 6

Newick tree

 
[
	9LVA_1:90.66,
	[
		6DHA_1:86,5QQX_1:86
	]:4.66
]

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 \((0.85)(0.8)(\frac{740 }{\log_{20} 740}-\frac{271}{\log_{20}271})=129.\)
Status Protein1 Protein2 d d1/2
Query variables 6DHA_1 5QQX_1 167 130.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]