CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3KTY_1 1JWF_1 8XOP_1 Letter Amino acid
30 10 22 A Alanine
13 6 9 R Arginine
5 2 11 H Histidine
1 3 1 W Tryptophan
3 3 0 C Cysteine
10 18 8 E Glutamic acid
7 8 17 I Isoleucine
1 14 8 K Lycine
5 7 6 N Asparagine
10 7 23 G Glycine
7 8 14 S Serine
2 3 6 Y Tyrosine
11 8 8 P Proline
11 7 13 T Threonine
13 8 6 V Valine
7 3 15 D Aspartic acid
7 6 9 Q Glutamine
21 17 20 L Leucine
4 4 9 M Methionine
5 5 5 F Phenylalanine 

3KTY_1|Chains A, B, C|Probable methyltransferase|Bordetella pertussis (520)
>1JWF_1|Chain A|ADP-ribosylation factor binding protein GGA1|Homo sapiens (9606)
>8XOP_1|Chains A, B, C, D, E, F, G|ATP-dependent Clp protease proteolytic subunit|Streptomyces hawaiiensis (67305)
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 \(w=f(c)\)
3KTY , Knot 79 173 0.78 40 117 166 
SNAMTQAFSRVRFIMTQPSHPGNVGSAARAIKTMGFGELVLVAPRFPDMTAQPEAVALASGALDVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAGVVAIVLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELRYALL
1JWF , Knot 74 147 0.83 40 114 143 
MEPAMEPETLEARINRATNPLNKELDWASINGFCEQLNEDFEGPPLATRLLAHKIQSPQEWEAIQALTVLETCMKSCGKRFHDEVGKFRFLNELIKVVSPKYLGSRTSEKVKNKILELLYSWTVGLPEEVKIAEAYQMLKKQGIVKS
8XOP , Knot 95 210 0.80 38 135 194 
MGSSHHHHHHSSGLVPRGSHMGLGDQVYNRLLNERIIFLGQPVDDDIANKITAQLLLLASDPEKDIYLYINSPGGSITAGMAIYDTMQYIKNDVVTIAMGLAAAMGQFLLSAGTPGKRFALPNAEILIHQPSAGLAGSASDIKIHAERLLHTKKRMAELTSQHTGQTIEQITRDSDRDRWFDAFEAKEYGLIDDVMTTAAGMPGGGGTGA

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 \(c\).

\(|P_{f(3KTY_1)}(2) \setminus P_{f(1JWF_1)}(2)|=76\), \(|P_{f(1JWF_1)}(2) \setminus P_{f(3KTY_1)}(2)|=73\). 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 1:00110011001011100100110110110110011110111111011010101011111011101100111000100111110111110001001111100100111110001000011111111100011100101010001001110100001011011011110100111
Pair \(Z_2\) Length of longest common subsequence
3KTY_1,1JWF_1 149 3
3KTY_1,8XOP_1 144 4
1JWF_1,8XOP_1 159 4

Newick tree

 
[
	1JWF_1:78.64,
	[
		3KTY_1:72,8XOP_1:72
	]:6.64
]

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 \((0.85)(0.8)(\frac{320 }{\log_{20} 320}-\frac{147}{\log_{20}147})=53.0\)
Status Protein1 Protein2 d d1/2
Query variables 3KTY_1 1JWF_1 63 61.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]