CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3AZX_1 8EIT_1 4KOT_1 Letter Amino acid
7 5 6 M Methionine
8 13 4 S Serine
30 16 8 E Glutamic acid
31 11 14 G Glycine
11 16 4 K Lycine
2 4 3 C Cysteine
13 4 5 H Histidine
11 14 7 F Phenylalanine
15 19 16 L Leucine
13 6 9 P Proline
13 14 4 T Threonine
11 3 2 W Tryptophan
18 14 9 V Valine
11 15 23 A Alanine
21 20 8 D Aspartic acid
6 7 10 Q Glutamine
16 6 7 Y Tyrosine
6 21 12 R Arginine
10 13 5 N Asparagine
19 17 6 I Isoleucine 

3AZX_1|Chains A, B|Laminarinase|Thermotoga maritima (243274)
>8EIT_1|Chain A|A modified Guanine nucleotide-binding protein G(q) subunit alpha|Homo sapiens (9606)
>4KOT_1|Chain A|Uncharacterized protein|Pseudomonas aeruginosa (208964)
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 \(w=f(c)\)
3AZX , Knot 122 272 0.83 40 178 259 
MEDEDKVEDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMNPETITGVEHHHHHH
8EIT , Knot 108 238 0.82 40 167 229 
MGSTLSAEDKAAVERSKMIDRNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNLREYNLV
4KOT , Knot 79 162 0.82 40 117 156 
GHMQLSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALIQMDKPLEP

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 \(c\).

\(|P_{f(3AZX_1)}(2) \setminus P_{f(8EIT_1)}(2)|=95\), \(|P_{f(8EIT_1)}(2) \setminus P_{f(3AZX_1)}(2)|=84\). 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 1:10000010010111000100111010110101101010111111010100000001110010111010000100001000000101000101010010101010110101111111111001101111001010110111000001010101110011101111001101110100010110101000010101010100110000110111011100111111011111011101000001100101001010001010010110000000
Pair \(Z_2\) Length of longest common subsequence
3AZX_1,8EIT_1 179 3
3AZX_1,4KOT_1 187 3
8EIT_1,4KOT_1 166 3

Newick tree

 
[
	3AZX_1:94.19,
	[
		8EIT_1:83,4KOT_1:83
	]:11.19
]

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 \((0.85)(0.8)(\frac{510 }{\log_{20} 510}-\frac{238}{\log_{20}238})=78.0\)
Status Protein1 Protein2 d d1/2
Query variables 3AZX_1 8EIT_1 100 94
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]