CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
9GZK_1 3HIQ_1 8FVH_1 Letter Amino acid
28 14 11 F Phenylalanine
11 2 3 W Tryptophan
25 14 5 Y Tyrosine
34 30 11 V Valine
1 0 1 C Cysteine
47 17 5 I Isoleucine
60 22 3 K Lycine
37 12 4 S Serine
18 17 2 P Proline
25 14 10 R Arginine
46 15 9 D Aspartic acid
16 20 12 Q Glutamine
12 6 5 M Methionine
9 9 0 H Histidine
55 34 8 L Leucine
35 24 2 T Threonine
33 25 12 A Alanine
43 27 6 N Asparagine
51 16 4 E Glutamic acid
38 27 10 G Glycine 

9GZK_1|Chains A, B, C, D, E, F|Glycosyltransferase|Listeria monocytogenes (1639)
>3HIQ_1|Chains A, B|Vacuolar saporin|Saponaria officinalis (3572)
>8FVH_1|Chains A, B, C, D, E, F|E217 collar protein gp28|Pseudomonas phage vB_PaeM_E217 (2034346)
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 \(w=f(c)\)
9GZK , Knot 245 624 0.84 40 267 573 
GMRNLKDRVLNSLKGNKKDIKISVVVPTYNTELEGLKNLMASIDKQTMNPDEYELVFVDDGSTTDTYERLQEFAETRPNMTVKQIENSGWGSRPRNIATKMAKGEYILYLDHDDTVFPETFERVYNFGKENNLDVVSGKEVRTNGWSWGWKQFSENNPHAEEMGIECLLPMTPHKFYKREFLLENDITFDDGARVLWEDVYFNSKAFIHGAKVGILADYPTYYWIATGANNSSSFGRDPHEKWNQINKLFNFFKDNIKEQRDLDFMLTHWYRSRVLGILGQWLLKNNNERIDIEFNYAKKLAEELIPAYISENLDKNNQVKDYLLRQGDLDSLKKLAQIDAGITALSYVEDAYFKEDKLFFKTSTKMTYEDKEDFFIEKTADRMERILPEEIKSKLPKEFFDYSDDLAEFTYEPSIKGRNSRATWKIDGSTSNVEVVNKKANLYKIEGEMSFSVQINDYILDAADKKQPWDIATRFTGLGYTSHRALTIGKILIKTALINNKTMIVYKNASGLISLDVGSSVRSIVEDSGVKREQILIDKTSGKVTIPLNEIHVFGESLIEGNAELKPVGISDADPINVKAKLIGEANKARVEVLLGDEKLSGEYHLVTNIQGKKDKQQIKITL
3HIQ , Knot 128 345 0.72 38 180 282 
MRGSHHHHHHGMASMTGGQQMGDLYDDDKDHPFTVIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFTVIIYELNLQGTTKAQYSTFLKQLRDDIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSNLAVAAYLAKNNNKQFRAYYFKGFQITTNQLNNLFPEATGVSNQQELGYGESYPQIQNAAGVTRQQAGLGIKKLAESMTKVNGVARVEKDEALFLLIVVQMVGEAARFKYIENLVLNNFDTAKEVEPVPDRVIILENNWGLLSRAAKTANNGVFQTPLVLTSYAVPGVEWRVTTVAEVEIGIFLNVDNN
8FVH , Knot 60 123 0.78 38 96 120 
IPGANLLRMAFGVIGTQIVRYRKFEQRVKNDQAQYVSMFGEPFDLAASVQRVRRDQYAQFNLEFQRNYVMIFANFDMVDLDRNMAGDQFLWTGRVFQLESQGSWFYQDGWGVCLAVDIGAAKA

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 \(c\).

\(|P_{f(9GZK_1)}(2) \setminus P_{f(3HIQ_1)}(2)|=121\), \(|P_{f(3HIQ_1)}(2) \setminus P_{f(9GZK_1)}(2)|=34\). 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 1:110010001100101000010101111000001011001110100001010000111100100000000100110001010100100011100100110011010011010000011100100100110000101101001000110111001000010100111001111010010000111000101001101110010100011101101111100100011101100000110010001001001101100010000010111001000011111101110000001010100100110011110100010000010001100101001001101011101100100101000011100000100000001110001001001110010001100110000011010001010100001010101000010110001010010101010101000110110000110110010111000001101101110011100001110001011101011001001100011000011100001010111001011100110101010111100101101010111010010101111000101000110010100000010101
Pair \(Z_2\) Length of longest common subsequence
9GZK_1,3HIQ_1 155 5
9GZK_1,8FVH_1 223 3
3HIQ_1,8FVH_1 168 3

Newick tree

 
[
	8FVH_1:10.83,
	[
		9GZK_1:77.5,3HIQ_1:77.5
	]:27.33
]

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 \((0.85)(0.8)(\frac{969 }{\log_{20} 969}-\frac{345}{\log_{20}345})=166.\)
Status Protein1 Protein2 d d1/2
Query variables 9GZK_1 3HIQ_1 213 153.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]