CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8YVD_1 8BYI_1 1JKM_1 Letter Amino acid
12 21 37 G Glycine
1 22 9 Y Tyrosine
7 27 27 R Arginine
2 15 2 Q Glutamine
2 7 11 H Histidine
1 27 18 S Serine
5 34 20 T Threonine
0 11 6 W Tryptophan
1 15 12 F Phenylalanine
19 27 46 A Alanine
4 29 30 D Aspartic acid
1 8 2 C Cysteine
7 16 22 E Glutamic acid
6 27 13 I Isoleucine
6 57 35 L Leucine
2 22 1 K Lycine
3 20 22 P Proline
2 20 8 N Asparagine
3 16 4 M Methionine
14 54 36 V Valine 

8YVD_1|Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O|Major carboxysome shell protein CsoS1A|Halothiobacillus neapolitanus (927)
>8BYI_1|Chains A, B, C, D, E|Acetylcholine receptor|Alvinella pompejana (6376)
>1JKM_1|Chains A, B|BREFELDIN A ESTERASE|Bacillus subtilis (1423)
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 \(w=f(c)\)
8YVD , Knot 47 98 0.73 38 71 94 
MADVTGIALGMIETRGLVPAIEAADAMTKAAEVRLVGRQFVGGGYVTVLVRGETGAVNAAVRAGADACERVGDGLVAAHIIARVHSEVENILPKAPQA
8BYI , Knot 198 475 0.85 40 242 447 
MAGSKVDKTLCRLGDITGLLIVLSVLVSRGLCQDCNNTNASSMADEKRLLKCILHDYDTAIRPVQNVSDVVNVALEVTVVKVIDLDEKEHVLTTNGWIYHEWNDFQLKWNPSDYSGLKKIRIPVDRIWTPDIVLFNNADESYRYVVDKLAVVYYTGKVMWVPHARLRSFCVLDLSRFPFDSQMCTLVFGSWTHDVSSVNVTLRNQSKVQYMIDGKEWQVTSVQPKRYQWTYNSNENYAGIITGIKLKRTSIYYQYVFIMPTVLLAFLTLLMPFIPPLGKERITYGIGLVLGCTLLLMMLSDRMPTELGNVPVVAAYLAYVFVMVAINLLFAIMAINMSMRDPKFGKVPGWVRWIFLTKLSKLVCLPVEPYTAVPADLAYEETAAARELLDMNNGTATADQRVSGSDTKPALDRTLEDIRRYLRLVATRTVVTPQLSHRDLVVQEWQQLTRVIDRLLFGSFLVLTVVITISMYAHY
1JKM , Knot 149 361 0.81 40 180 338 
YTPPGRLGDESSGPRTDPRFSPAMVEALATFGLDAVAAAPPVSASDDLPTVLAAVGASHDGFQAVYDSIALDLPTDRDDVETSTETILGVDGNEITLHVFRPAGVEGVLPGLVYTHGGGMTILTTDNRVHRRWCTDLAAAGSVVVMVDFRNAWTAEGHHPFPSGVEDCLAAVLWVDEHRESLGLSGVVVQGESGGGNLAIATTLLAKRRGRLDAIDGVYASIPYISGGYAWDHERRLTELPSLVENDGYFIENGGMALLVRAYDPTGEHAEDPIAWPYFASEDELRGLPPFVVAVNELDPLRDEGIAFARRLARAGVDVAARVNIGLVHGADVIFRHWLPAALESTVRDVAGFAADRARLR

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 \(c\).

\(|P_{f(8YVD_1)}(2) \setminus P_{f(8BYI_1)}(2)|=27\), \(|P_{f(8BYI_1)}(2) \setminus P_{f(8YVD_1)}(2)|=198\). 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 1:11010111111100011111101101100110101110011111010111010011101110111010001101111101110100010011101101
Pair \(Z_2\) Length of longest common subsequence
8YVD_1,8BYI_1 225 3
8YVD_1,1JKM_1 145 3
8BYI_1,1JKM_1 172 4

Newick tree

 
[
	8BYI_1:10.77,
	[
		8YVD_1:72.5,1JKM_1:72.5
	]:35.27
]

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 \((0.85)(0.8)(\frac{573 }{\log_{20} 573}-\frac{98}{\log_{20}98})=140.\)
Status Protein1 Protein2 d d1/2
Query variables 8YVD_1 8BYI_1 180 107.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: