CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2ZXF_1 6YJE_1 9DRF_1 Letter Amino acid
52 48 6 K Lycine
19 10 5 M Methionine
38 14 7 F Phenylalanine
21 6 6 Y Tyrosine
52 33 17 V Valine
33 18 10 T Threonine
36 6 16 R Arginine
58 33 25 E Glutamic acid
21 7 12 H Histidine
35 33 14 I Isoleucine
58 40 20 L Leucine
34 24 13 S Serine
42 23 9 D Aspartic acid
12 3 0 C Cysteine
30 10 7 Q Glutamine
4 2 4 W Tryptophan
50 31 19 A Alanine
25 26 6 N Asparagine
43 38 16 G Glycine
30 11 6 P Proline 

2ZXF_1|Chain A|Glycyl-tRNA synthetase|Homo sapiens (9606)
>6YJE_1|Chain A|Phosphoglycerate kinase|Plasmodium vivax (5855)
>9DRF_1|Chains A, B, C, D, E, F, G, H|ADP-ribose pyrophosphatase|Klebsiella pneumoniae (573)
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 \(w=f(c)\)
2ZXF , Knot 265 693 0.83 40 288 648 
MDGAGAEEVLAPLRLAVRQQGDLVRKLKEDKAPQVDVDKAVAELKARKRVLEAKELALQPKDDIVDRAKMEDTLKRRFFYDQAFAIYGGVSGLYDFGPVGCALKNNIIQTWRQHFIQEEQILEIDCTMLTPEPVLKTSGHVDKFADFMVKDVKNGECFRADHLLKAHLQKLMSDKKCSVEKKSEMESVLAQLDNYGQQELADLFVNYNVKSPITGNDLSPPVSFNLMFKTFIGPGGNMPGYLRPETAQGIFLNFKRLLEFNQGKLPFAAAQIGNSFRNEISPRSGLIRVREFTMAEIEHFVDPSEKDHPKFQNVADLHLYLYSAKAQVSGQSARKMRLGDAVEQGVINNTVLGYFIGRIYLYLTKVGISPDKLRFRQHMENEMAHYACDCWDAESKTSYGWIEIVGCADRSCYDLSCHARATKVPLVAEKPLKEPKTVNVVQFEPSKGAIGKAYKKDAKLVMEYLAICDECYITEMEMLLNEKGEFTIETEGKTFQLTKDMINVKRFQKTLYVEEVVPNVIEPSFGLGRIMYTVFEHTFHVREGDEQRTFFSFPAVVAPFKCSVLPLSQNQEFMPFVKELSEALTRHGVSHKVDDSSGSIGRRYARTDEIGVAFGVTIDFDTVNKTPHTATLRDRDSMRQIRAEISELPSIVQDLANGNITWADVEARYPLFEGQETGKKETIEELEHHHHHH
6YJE , Knot 170 416 0.82 40 204 388 
SLGNKLSITDVKAIQGKKVLVRVDFNVPIENGVIKDTNRITATLPTIHHLKKEGAAKIILISHCGRPDGTKNLKYTLKPVAETLGTLLGEEVLFLSDCVGEEVAAQINQAKDNSVILLENLRFHVEEEGKGVDAAGNKIKASKEDMEKFQNELTKLGDVFINDAFGTAHRAHSSMVGIKMNVKASGFLMKKELEYFSKALENPQRPLLAILGGAKVSDKIQLIKNLLDKVDKMIIGGGMAYTFKYVLNNMKIGDSLFDEAGSKIVNEIMEKAKAKNVEIYLPVDFKVADKFDNNANTKVVTDEEGIEDKWMGLDAGPKSIENYKDVILSSKTIIWNGPQGVFEMPNFAKGSIECLNLVIEATKKGAISIVGGGDTASLVEQQQKKNEISHVSTGGGASLELLEGKELPGVVALSSK
9DRF , Knot 98 218 0.80 38 148 210 
MAHHHHHHMSKPTQQGITFSKNDVEIIARETLYRGFFSLDLYRFRHRLFNGGMSGEITREIFERGHAAVLLPFDPVRDEVVLVEQIRIAAYDTSESPWLLEMVAGMIEAGETVEDVARREALEEAGLEVGRTKPILSYLASPGGTSERLSILVGEVDASTAKGIHGLAEENEDIRVHVVSREQAYQWVEEGKIDNAASVIALQWLQLHYHNLRNEWTK

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 \(c\).

\(|P_{f(2ZXF_1)}(2) \setminus P_{f(6YJE_1)}(2)|=112\), \(|P_{f(6YJE_1)}(2) \setminus P_{f(2ZXF_1)}(2)|=28\). 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 1:101111001111101110001011001000011010100111010100011010011101000110010100010001100011110111011001111101100011001000110000110100011010111000101001101110010010010100110101001100000010000010011101000100011011100010011010010111010111001111110111010100101111010011010010111111011001000101001110100101101001101000001010011010101001010101001001011011001110001110111010101001110100101000100011001000101000000111011101000000100010100111110011001001011010100111101000010111001110000010010111000101010001001010001101001000101001110110101111011001100010100100000110111111110001111000001111100100110001100010000101100010000111111101010010001001010000010010101001101100110101011010100111010001000010010000000
Pair \(Z_2\) Length of longest common subsequence
2ZXF_1,6YJE_1 140 4
2ZXF_1,9DRF_1 194 6
6YJE_1,9DRF_1 158 4

Newick tree

 
[
	9DRF_1:93.80,
	[
		2ZXF_1:70,6YJE_1:70
	]:23.80
]

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 \((0.85)(0.8)(\frac{1109 }{\log_{20} 1109}-\frac{416}{\log_{20}416})=181.\)
Status Protein1 Protein2 d d1/2
Query variables 2ZXF_1 6YJE_1 229 181
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]