CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8JVE_1 4QHJ_1 6YMI_1 Letter Amino acid
2 0 9 C Cysteine
16 18 0 L Leucine
5 6 0 F Phenylalanine
7 3 0 T Threonine
4 4 0 Y Tyrosine
4 0 0 V Valine
11 4 4 A Alanine
6 13 0 N Asparagine
9 3 0 D Aspartic acid
8 1 0 Q Glutamine
5 1 0 M Methionine
3 0 0 W Tryptophan
10 3 0 R Arginine
9 10 0 E Glutamic acid
3 3 0 H Histidine
17 3 0 P Proline
8 4 0 S Serine
7 1 8 G Glycine
11 16 0 I Isoleucine
11 17 0 K Lycine 

8JVE_1|Chain A|Ubiquitin-conjugating enzyme E2 T|Homo sapiens (9606)
>4QHJ_1|Chains A, B|Uncharacterized protein MJ1213|Methanocaldococcus jannaschii (243232)
>6YMI_1|Chains A, C, E[auth F], G[auth I], I[auth M], K[auth O]|Chains: A,C,F,I,M,O|Roseobacter sp. (1907202)
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 \(w=f(c)\)
8JVE , Knot 77 156 0.83 40 128 152 
GSMQRASRLKRELHMLATEPPPGITCWQDKDQMDDLRAQILGGANTPYEKGVFKLEVIIPERYPFEPPQIRFLTPIYHPNIDSAGRICLDVLKLPPKGAWRPSLNIATVLTSIQLLMSEPNPDDPLMADISSEFKYNKPAFLKNARQWTEKHARQK
4QHJ , Knot 51 110 0.72 34 73 102 
MKDRKILNEILSNTINELNLNDKKANIKIKIKPLKRKIASISLTNKTIYINKNILPYLSDEEIRFILAHELLHLKYGKYHINEFEEELLFLFPNKEAILFNLINKLFQKK
6YMI , Knot 13 26 0.54 8 13 23 
GGUCACAACGGCUUCCUGGCGUGACC

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 \(c\).

\(|P_{f(8JVE_1)}(2) \setminus P_{f(4QHJ_1)}(2)|=92\), \(|P_{f(4QHJ_1)}(2) \setminus P_{f(8JVE_1)}(2)|=37\). 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 1:101001001000101110011111001000001001010111110010001110101111000110110101101100101001101010110111011101010110110010111001010011110100010000111100100100001000
Pair \(Z_2\) Length of longest common subsequence
8JVE_1,4QHJ_1 129 3
8JVE_1,6YMI_1 137 2
4QHJ_1,6YMI_1 86 1

Newick tree

 
[
	8JVE_1:72.70,
	[
		4QHJ_1:43,6YMI_1:43
	]:29.70
]

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 \((0.85)(0.8)(\frac{266 }{\log_{20} 266}-\frac{110}{\log_{20}110})=49.3\)
Status Protein1 Protein2 d d1/2
Query variables 8JVE_1 4QHJ_1 62 51.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]