CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7QPP_1 5KVY_1 3JZZ_1 Letter Amino acid
13 10 6 R Arginine
34 13 10 L Leucine
9 10 3 M Methionine
8 8 3 Y Tyrosine
12 23 23 A Alanine
14 11 2 K Lycine
8 9 3 F Phenylalanine
14 11 6 P Proline
25 18 12 S Serine
10 9 23 T Threonine
1 1 2 W Tryptophan
17 11 3 E Glutamic acid
12 22 13 G Glycine
10 4 0 H Histidine
15 13 10 V Valine
14 14 6 Q Glutamine
16 11 7 D Aspartic acid
6 0 2 C Cysteine
18 13 6 I Isoleucine
7 5 8 N Asparagine 

7QPP_1|Chain A|Vitamin D3 receptor|Homo sapiens (9606)
>5KVY_1|Chains A, B|Poly(U)-binding-splicing factor PUF60|Homo sapiens (9606)
>3JZZ_1|Chain A|Type IV pilin structural subunit|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 \(w=f(c)\)
7QPP , Knot 117 263 0.82 40 174 250 
GSHMDSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFGNEIS
5KVY , Knot 95 216 0.78 38 143 205 
GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG
3JZZ , Knot 71 148 0.80 38 103 139 
DPFTVRTRVSEGLVLAEPAKLMISTDGSASTADLTRATTTWNQQSNNLGASSKYVTSVLMDAGNTGVITITYVADQVGLPTAGNTLILSPYINDGNTRTALATAVAAGTRGTIDWACTSASNATATAQGFTGMAAGSVPQEFAPAQCR

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 \(c\).

\(|P_{f(7QPP_1)}(2) \setminus P_{f(5KVY_1)}(2)|=99\), \(|P_{f(5KVY_1)}(2) \setminus P_{f(7QPP_1)}(2)|=68\). 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 1:10010010101000000111111010000001000010010111010011101010100101110110110001001111101111100100000111100011011110000010100101001000000010010011001011011101011100101000001111110110100111001111011000100010001000011110011010110011010010000000000101010001010111101110010
Pair \(Z_2\) Length of longest common subsequence
7QPP_1,5KVY_1 167 4
7QPP_1,3JZZ_1 161 4
5KVY_1,3JZZ_1 154 3

Newick tree

 
[
	7QPP_1:83.61,
	[
		3JZZ_1:77,5KVY_1:77
	]:6.61
]

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 \((0.85)(0.8)(\frac{479 }{\log_{20} 479}-\frac{216}{\log_{20}216})=76.2\)
Status Protein1 Protein2 d d1/2
Query variables 7QPP_1 5KVY_1 99 88.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]