CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5FCK_1 8SMD_1 3BPB_1 Letter Amino acid
16 6 12 D Aspartic acid
14 2 13 P Proline
8 6 13 T Threonine
22 8 18 V Valine
8 1 5 C Cysteine
6 10 10 K Lycine
0 3 9 F Phenylalanine
4 4 9 Y Tyrosine
4 1 1 W Tryptophan
18 10 20 R Arginine
5 7 7 N Asparagine
8 5 5 Q Glutamine
22 9 19 G Glycine
10 3 6 H Histidine
6 7 21 I Isoleucine
27 6 21 A Alanine
9 14 26 E Glutamic acid
27 8 19 L Leucine
2 4 6 M Methionine
16 11 14 S Serine 

5FCK_1|Chain A|Complement factor D|Homo sapiens (9606)
>8SMD_1|Chains A, B|ABC transporter ATPase|Clostridium botulinum (1491)
>3BPB_1|Chains A, B|dimethylarginine dimethylaminohydrolase|Pseudomonas aeruginosa (287)
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 \(w=f(c)\)
5FCK , Knot 103 232 0.80 38 145 218 
ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASAAA
8SMD , Knot 62 125 0.79 40 101 123 
SMKELSTIQKREKLNTVERIGSEGPGGAYHEYVIKSNSMDSQGNYDVYETIKFQKGARKEEKSQHGVIDSDLLEIVRDRLKSFQAGPFSSRENACALTHVEEALMWMNRRVEDRIERNVLGTNTK
3BPB , Knot 115 254 0.83 40 164 247 
MFKHIIARTPARSLVDGLTSSHLGKPDYAKALEQHNAYIRALQTCDVDITLLPPDERFPDSVFVEDPVLCTSRCAIITRPGAESRRGETEIIEETVQRFYPGKVERIEAPGTVEAGDIMMVGDHFYIGESARTNAEGARQMIAILEKHGLSGSVVRLEKVLGLKTGLAYLEHNNLLAAGEFVSKPEFQDFNIIEIPEEESYAANCIWVNERVIMPAGYPRTREKIARLGYRVIEVDTSEYRKIDGGVSCMSLRF

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 \(c\).

\(|P_{f(5FCK_1)}(2) \setminus P_{f(8SMD_1)}(2)|=97\), \(|P_{f(8SMD_1)}(2) \setminus P_{f(5FCK_1)}(2)|=53\). 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 1:1111001010101011010101101011111100111011001001101010111110010010100010011011101000100100011110100010111110111100100011110100111111100110010010011111100100000000011100011010000000001001111101111011100100101000011100011001111001110111
Pair \(Z_2\) Length of longest common subsequence
5FCK_1,8SMD_1 150 3
5FCK_1,3BPB_1 147 4
8SMD_1,3BPB_1 165 4

Newick tree

 
[
	8SMD_1:80.54,
	[
		5FCK_1:73.5,3BPB_1:73.5
	]:7.04
]

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 \((0.85)(0.8)(\frac{357 }{\log_{20} 357}-\frac{125}{\log_{20}125})=70.9\)
Status Protein1 Protein2 d d1/2
Query variables 5FCK_1 8SMD_1 86 68
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]