CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6TWE_1 5PUK_1 8OMP_1 Letter Amino acid
8 5 12 T Threonine
8 10 17 V Valine
10 5 9 I Isoleucine
11 13 19 D Aspartic acid
6 8 11 Q Glutamine
9 13 13 E Glutamic acid
17 7 22 G Glycine
2 7 2 M Methionine
11 7 18 S Serine
5 14 7 R Arginine
9 6 12 F Phenylalanine
5 0 7 W Tryptophan
7 5 8 Y Tyrosine
9 6 24 K Lycine
7 4 10 N Asparagine
2 1 1 C Cysteine
10 10 12 H Histidine
12 18 26 L Leucine
10 6 17 P Proline
14 11 13 A Alanine 

6TWE_1|Chain A|Putative chitin binding protein|Bacillus licheniformis DSM 13 = ATCC 14580 (279010)
>5PUK_1|Chains A, B|Bromodomain-containing protein 1|Homo sapiens (9606)
>8OMP_1|Chain A|Carbonic anhydrase 2|Homo sapiens (9606)
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 \(w=f(c)\)
6TWE , Knot 85 172 0.84 40 138 169 
HGFIEKPGSRAALCSEAFGFLNLNCGSVMYEPQSLEAKKGFPHSGPADGQIASAGGLFGGILDQQSENRWFKHIMTGGEHTFTWTYTAPHNTSQWHYYITKKGWDPDKPLKRADFELIGAVPHDGSPASRNLSHHIYIPEDRLGYHVILAVWDVADTENAFYQVIDVDLVNK
5PUK , Knot 74 156 0.79 38 120 151 
MHHHHHHSSGVDLGTENLYFQSMEQVAMELRLTELTRLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDQGGVVLRQARREVDSIGLEEASGMHLPERPA
8OMP , Knot 112 260 0.79 40 176 249 
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK

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 \(c\).

\(|P_{f(6TWE_1)}(2) \setminus P_{f(5PUK_1)}(2)|=91\), \(|P_{f(5PUK_1)}(2) \setminus P_{f(6TWE_1)}(2)|=73\). 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 1:0111001100111000111110100101100100101001110011101011011111111100000001100110110001010001100000100010001101001100101011111100101100010001011000110011111101100001100110101100
Pair \(Z_2\) Length of longest common subsequence
6TWE_1,5PUK_1 164 3
6TWE_1,8OMP_1 164 3
5PUK_1,8OMP_1 158 3

Newick tree

 
[
	6TWE_1:82.97,
	[
		5PUK_1:79,8OMP_1:79
	]:3.97
]

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 \((0.85)(0.8)(\frac{328 }{\log_{20} 328}-\frac{156}{\log_{20}156})=52.4\)
Status Protein1 Protein2 d d1/2
Query variables 6TWE_1 5PUK_1 68 63.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]