CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5DMH_1 5QMN_1 1IZE_1 Letter Amino acid
19 12 9 E Glutamic acid
49 13 37 G Glycine
6 2 0 C Cysteine
26 12 32 D Aspartic acid
6 6 0 M Methionine
2 2 3 W Tryptophan
75 17 24 A Alanine
14 3 2 H Histidine
16 5 15 I Isoleucine
53 12 15 L Leucine
7 17 9 K Lycine
16 11 19 F Phenylalanine
21 7 11 P Proline
25 9 30 T Threonine
30 3 2 R Arginine
17 14 14 Q Glutamine
21 8 49 S Serine
4 8 18 Y Tyrosine
36 21 24 V Valine
11 7 10 N Asparagine 

5DMH_1|Chains A, B|Uncharacterized protein conserved in bacteria|Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (381666)
>5QMN_1|Chains A, B|Thiol:disulfide interchange protein|Escherichia coli K-12 (83333)
>1IZE_1|Chain A|aspartic proteinase|Aspergillus oryzae (5062)
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 \(w=f(c)\)
5DMH , Knot 177 454 0.79 40 191 392 
MHHHHHHSSGVDLGTENLYFQSMTAGTLAHRPLLGCIADDFTGATDLANTLVRNGMRTVQTIGLPDVGAVQDIGEADALVVALKSRTIPAVEAVAQSLAALQWLRAQGCRQFVFKYCSTFDSTDAGNIGPVAEALLAALDSDFTIACPAFPENGRTIFRGHLFVGDALLNESGMEHHPLTPMTDASLVRVLQRQSKNKVGLLRYDAVARGAHATAERIAALRSDGVRMAIADAVSDADLFTLGEACANLPLITGGSGIALGLPENFRRAGLLPQRGDAASVPAIDGPGVVLAGSASRATNGQVARWLEQGRPALRIDPLALARGEAVADAALAFAAGHGEPVLIYATSSPDEVKAVQAELGVERAGHLVEQCLATVAAGLLARGTRRFVVAGGETSGAVVQALGVRALRIGAQIAPGVPATVTLDAKPLALALKSGNFGGPDFFDEALRQLGGH
5QMN , Knot 86 189 0.79 40 134 185 
AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK
1IZE , Knot 132 323 0.78 36 159 293 
AATGSVTTNPTSNDEEYITQVTVGDDTLGLDFDTGSADLWVFSSQTPSSERSGHDYYTPGSSAQKIDGATWSISYGDGSSASGDVYKDKVTVGGVSYDSQAVESAEKVSSEFTQDTANDGLLGLAFSSINTVQPTPQKTFFDNVKSSLSEPIFAVALKHNAPGVYDFGYTDSSKYTGSITYTDVDNSQGFWGFTADGYSIGSDSSSDSITGIADTGTTLLLLDDSIVDAYYEQVNGASYDSSQGGYVFPSSASLPDFSVTIGDYTATVPGEYISFADVGNGQTFGGIQSNSGIGFSIFGDVFLKSQYVVFDASGPRLGFAAQA

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 \(c\).

\(|P_{f(5DMH_1)}(2) \setminus P_{f(5QMN_1)}(2)|=119\), \(|P_{f(5QMN_1)}(2) \setminus P_{f(5DMH_1)}(2)|=62\). 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 1:1000000001101100010100101101100111101100101100110011001100100111101111001101011111100001111011100111101101010001110000010000110111110111111000101101111001001101011110111000110001101100101101100000001111000111011010100111100011011110110010110110101011110110111111100100111110010110111101111111101001001011011001011101011111010111011111111010111101000100101101011100110110001101111111010001111110001111011110110111011111110101010111111001011110110011001110
Pair \(Z_2\) Length of longest common subsequence
5DMH_1,5QMN_1 181 4
5DMH_1,1IZE_1 156 4
5QMN_1,1IZE_1 147 5

Newick tree

 
[
	5DMH_1:87.83,
	[
		1IZE_1:73.5,5QMN_1:73.5
	]:14.33
]

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 \((0.85)(0.8)(\frac{643 }{\log_{20} 643}-\frac{189}{\log_{20}189})=129.\)
Status Protein1 Protein2 d d1/2
Query variables 5DMH_1 5QMN_1 155 110.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]