CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6ZQQ_1 2DNW_1 4ALL_1 Letter Amino acid
9 3 23 A Alanine
2 1 0 C Cysteine
18 8 26 G Glycine
9 1 15 N Asparagine
9 12 12 D Aspartic acid
10 3 9 Q Glutamine
15 1 17 H Histidine
12 8 19 I Isoleucine
11 6 5 P Proline
9 1 10 T Threonine
6 0 0 W Tryptophan
13 6 21 V Valine
12 7 17 K Lycine
4 5 6 M Methionine
6 3 9 F Phenylalanine
10 1 12 R Arginine
20 9 22 E Glutamic acid
16 10 26 L Leucine
14 10 19 S Serine
7 4 9 Y Tyrosine 

6ZQQ_1|Chains A, B, C, D|PMT3 isoform 1|Saccharomyces cerevisiae (4932)
>2DNW_1|Chain A|Acyl carrier protein|Homo sapiens (9606)
>4ALL_1|Chains A, B, C, D|ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]|STAPHYLOCOCCUS AUREUS (1280)
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 \(w=f(c)\)
6ZQQ , Knot 99 212 0.83 40 155 202 
MKHHHHHHPMGPRDVALGSSIISIKNQALGGALLHSHVQPFPEGSEQQQVTVYGYSDANNEWFFQRIRGVEPWTDAENKTIEFVKGGEMYRLMHRLTGKNLHTHEVPAPISKSEYEVSAYGDVDLGDYKDNWIIEIVEQVGEEDPTLLHPLSTSFRIKNSILGCYLAQSGKHLPEWGFRQGEVVCLKHASKRDKRTWWNIETHENERLPQGE
2DNW , Knot 49 99 0.75 38 81 93 
GSSGSSGMPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYESGPSSG
4ALL , Knot 118 277 0.79 36 169 261 
MGHHHHHHHHHHSSGHIEGRHMLNLENKTYVIMGIANKRSIAFGVAKVLDQLGAKLVFTYRKERSRKELEKLLEQLNQPEAHLYQIDVQSDEEVINGFEQIGKDVGNIDGVYHSIAFANMEDLRGRFSETSREGFLLAQDISSYSLTIVAHEAKKLMPEGGSIVATTYLGGEFAVQNYNVMGVAKASLEANVKYLALDLGPDNIRVNAISAGPIRTLSAKGVGGFNTILKEIEERAPLKRNVDQVEVGKTAAYLLSDLSSGVTGENIHVDSGFHAIK

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 \(c\).

\(|P_{f(6ZQQ_1)}(2) \setminus P_{f(2DNW_1)}(2)|=119\), \(|P_{f(2DNW_1)}(2) \setminus P_{f(6ZQQ_1)}(2)|=45\). 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 1:10000000111100111100110100011111110001011101000001010100010001110010110110010000101101101001100101001000011111000000101010101100000111011001100010110110001010001110011001001101110010110100100000001101000000011010
Pair \(Z_2\) Length of longest common subsequence
6ZQQ_1,2DNW_1 164 3
6ZQQ_1,4ALL_1 156 6
2DNW_1,4ALL_1 150 4

Newick tree

 
[
	6ZQQ_1:81.63,
	[
		4ALL_1:75,2DNW_1:75
	]:6.63
]

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 \((0.85)(0.8)(\frac{311 }{\log_{20} 311}-\frac{99}{\log_{20}99})=66.4\)
Status Protein1 Protein2 d d1/2
Query variables 6ZQQ_1 2DNW_1 86 62
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]