CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7CZM_1 5FEY_1 5DIO_1 Letter Amino acid
10 3 11 V Valine
1 7 1 C Cysteine
3 3 5 Q Glutamine
3 8 9 T Threonine
4 0 5 Y Tyrosine
4 7 14 I Isoleucine
11 15 9 L Leucine
11 4 8 K Lycine
2 0 3 W Tryptophan
3 9 5 H Histidine
1 2 6 M Methionine
9 7 7 S Serine
7 3 9 A Alanine
3 3 8 N Asparagine
5 3 9 D Aspartic acid
7 7 5 E Glutamic acid
7 5 4 R Arginine
6 3 6 G Glycine
6 2 4 F Phenylalanine
5 3 5 P Proline 

7CZM_1|Chains A, B|RB1-inducible coiled-coil protein 1|Homo sapiens (9606)
>5FEY_1|Chains A, B|E3 ubiquitin-protein ligase TRIM32|Homo sapiens (9606)
>5DIO_1|Chains A, B|Thioesterase|Legionella pneumophila (446)
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 \(w=f(c)\)
7CZM , Knot 57 108 0.82 40 89 104 
SEFSRHSEKIAIRDFQVGDLVLIILDERHDNYVLFTVSPTLYFLHSESLPALDLKPGEGASGASRRPWVLGKVMEKEYCQAKKAQNRFKVPLGTKFYRVKAVSWNKKV
5FEY , Knot 50 94 0.80 36 76 88 
MSHLNLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSLTQLTDNLTVLKIIDTAGLSEHHHHHH
5DIO , Knot 67 133 0.82 40 108 131 
SNAMTEINKIIHKKTFDIAWGDMAALGHVNNARYFDYFQEARIDWLRELDIKMTGQTGPVVIHVACTFLKPIVYPATVTIHSKVNSLGNSSMIMDHDLYQEETLMAQGVSKIVWIDYTQNKSVPLPDIIRNLV

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 \(c\).

\(|P_{f(7CZM_1)}(2) \setminus P_{f(5FEY_1)}(2)|=72\), \(|P_{f(5FEY_1)}(2) \setminus P_{f(7CZM_1)}(2)|=59\). 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 1:001000000111001011011111100000001110101010110000111101011011011000111110110000001001000101111001001011010001
Pair \(Z_2\) Length of longest common subsequence
7CZM_1,5FEY_1 131 2
7CZM_1,5DIO_1 135 3
5FEY_1,5DIO_1 140 3

Newick tree

 
[
	5DIO_1:69.81,
	[
		7CZM_1:65.5,5FEY_1:65.5
	]:4.31
]

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 \((0.85)(0.8)(\frac{202 }{\log_{20} 202}-\frac{94}{\log_{20}94})=35.3\)
Status Protein1 Protein2 d d1/2
Query variables 7CZM_1 5FEY_1 46 42.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]