CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9LNV_1 4WKZ_1 2ZJY_1 Letter Amino acid
20 9 19 F Phenylalanine
20 6 6 P Proline
36 26 32 A Alanine
27 25 26 D Aspartic acid
37 18 28 E Glutamic acid
19 16 29 K Lycine
29 27 21 T Threonine
21 5 18 R Arginine
23 15 17 S Serine
4 1 3 W Tryptophan
18 15 13 Y Tyrosine
16 13 15 N Asparagine
12 0 10 C Cysteine
16 3 13 Q Glutamine
36 15 19 G Glycine
13 1 6 H Histidine
27 9 26 I Isoleucine
32 14 27 L Leucine
10 3 9 M Methionine
34 22 19 V Valine 

9LNV_1|Chains A, B[auth C]|Detyrosinated tubulin alpha-1B chain|Sus scrofa (9823)
>4WKZ_1|Chain A|Putative cellulose-binding protein|Ruminococcus flavefaciens (641112)
>2ZJY_1|Chain A|Guanine nucleotide-binding protein G(i), alpha-1 subunit|Rattus norvegicus (10116)
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 \(w=f(c)\)
9LNV , Knot 192 450 0.87 40 257 425 
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEE
4WKZ , Knot 105 243 0.79 38 144 224 
MGSSNTVTSAVKTQYVEIESVMGFYFNTEDKFDTAQIKKAVLHTVYNEGYTGDDGVAVVLREYESEPVDITAELTFGDATPANTYKAVENKFDYEIPVYYNNATLKDAEGNDATVTVYIGLKGDTDLNNIVDGRDATATLTYYAATSTDGKDATTVALSPSTLVGGNPESVYDDFSAFLSDVKVDAGKELTRFAKKAERLIDGRDASSILTFYTKSSVDQYKDMAANEPNKLWDIVTADAEEE
2ZJY , Knot 154 356 0.84 40 210 337 
GPMGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDAARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLPDCGLF

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 \(c\).

\(|P_{f(9LNV_1)}(2) \setminus P_{f(4WKZ_1)}(2)|=149\), \(|P_{f(4WKZ_1)}(2) \setminus P_{f(9LNV_1)}(2)|=36\). 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 1:100010101101110110101010010011010101100001111000100110001110011011110101011001001000011010011010001100010100011001101110010011000011011111001111010110011100101001000010101011101001110100011000001000001111000110010000101001000010011001100101010101110101001000111010101111001111010010000101101001010110011000100100110011001011100101111010000010110101011011100011011111011010011011000011101110100010110100111010110110010100100011110000001110010101000100
Pair \(Z_2\) Length of longest common subsequence
9LNV_1,4WKZ_1 185 4
9LNV_1,2ZJY_1 177 4
4WKZ_1,2ZJY_1 152 4

Newick tree

 
[
	9LNV_1:94.87,
	[
		2ZJY_1:76,4WKZ_1:76
	]:18.87
]

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 \((0.85)(0.8)(\frac{693 }{\log_{20} 693}-\frac{243}{\log_{20}243})=125.\)
Status Protein1 Protein2 d d1/2
Query variables 9LNV_1 4WKZ_1 163 122.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]