CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3JPT_1 5QDH_1 7QWN_1 Letter Amino acid
9 11 12 H Histidine
23 18 25 I Isoleucine
14 22 26 P Proline
12 9 9 Y Tyrosine
18 13 44 A Alanine
19 19 25 R Arginine
13 14 16 Q Glutamine
7 11 11 M Methionine
14 14 23 F Phenylalanine
19 13 17 T Threonine
18 17 25 V Valine
21 18 28 D Aspartic acid
27 30 30 E Glutamic acid
26 29 26 L Leucine
21 25 18 S Serine
1 6 8 W Tryptophan
3 4 3 C Cysteine
22 14 33 G Glycine
36 23 18 K Lycine
12 11 20 N Asparagine

3JPT_1|Chain A|DNA polymerase beta|Homo sapiens (9606)
>5QDH_1|Chain A|Tyrosine-protein phosphatase non-receptor type 1|Homo sapiens (9606)
>7QWN_1|Chains A, B, C|Steroid C26-monooxygenase|Mycobacterium tuberculosis H37Rv (83332)
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 \(w=f(c)\)
3JPT , Knot 146 335 0.84 40 199 321
MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
5QDH , Knot 141 321 0.84 40 205 309
MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
7QWN , Knot 177 417 0.85 40 235 400
NGPSPNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPGKGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMDAPHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIAGLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIVTQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPETAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILRNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKHWQVDYTGRCPVA

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 \(c\).

\(|P_{f(3JPT_1)}(2) \setminus P_{f(5QDH_1)}(2)|=75\), \(|P_{f(5QDH_1)}(2) \setminus P_{f(3JPT_1)}(2)|=81\). 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 1:10000110001011100110011010001001100001000110111001001001101001111100110010011101010010010000000010110010111101100110011001001000000100000111001101000110001101001110010010000110101010011000101011100101000000010110011001001011000100100011110011000000001000101011100000011101010011000101011001101000010111101111011110000011001010000100000
Pair \(Z_2\) Length of longest common subsequence
3JPT_1,5QDH_1 156 3
3JPT_1,7QWN_1 164 3
5QDH_1,7QWN_1 164 4

Newick tree

 
[
	7QWN_1:83.29,
	[
		3JPT_1:78,5QDH_1:78
	]:5.29
]

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 \((0.85)(0.8)(\frac{656 }{\log_{20} 656}-\frac{321}{\log_{20}321})=92.7\)
Status Protein1 Protein2 d d1/2
Query variables 3JPT_1 5QDH_1 116 112.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]