CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3UJP_1 5NKP_1 1WZI_1 Letter Amino acid
17 9 15 P Proline
13 24 11 S Serine
12 16 7 Y Tyrosine
9 18 20 R Arginine
28 12 24 E Glutamic acid
22 19 30 L Leucine
28 25 47 A Alanine
20 34 28 G Glycine
15 6 16 I Isoleucine
30 37 27 V Valine
18 13 11 N Asparagine
18 8 12 Q Glutamine
2 3 4 H Histidine
13 9 17 K Lycine
5 9 11 M Methionine
10 6 11 F Phenylalanine
24 16 14 T Threonine
3 6 4 W Tryptophan
17 16 17 D Aspartic acid
3 6 1 C Cysteine 

3UJP_1|Chains A, B, C|Mn transporter subunit|Synechocystis sp. PCC 6803 (1148)
>5NKP_1|Chains A, B|Kelch-like protein 3|Homo sapiens (9606)
>1WZI_1|Chains A, B|Malate dehydrogenase|Thermus thermophilus (274)
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 \(w=f(c)\)
3UJP , Knot 133 307 0.82 40 187 297 
GCGTAEVTTSNAPSEEVTAVTTEVQGETEEKKKVLTTFTVLADMVQNVAGDKLVVESITRIGAEIHGYEPTPSDIVKAQDADLILYNGMNLERWFEQFLGNVKDVPSVVLTEGIEPIPIADGPYTDKPNPHAWMSPRNALVYVENIRQAFVELDPDNAKYYNANAAVYSEQLKAIDRQLGADLEQVPANQRFLVSCEGAFSYLARDYGMEEIYMWPINAEQQFTPKQVQTVIEEVKTNNVPTIFCESTVSDKGQKQVAQATGARFGGNLYVDSLSTEEGPVPTFLDLLEYDARVITNGLLAGTNAQQ
5NKP , Knot 120 292 0.77 40 166 252 
SMSLPKVMIVVGGQAPKAIRSVECYDFEEDRWDQIAELPSRRCRAGVVFMAGHVYAVGGFNGSLRVRTVDVYDGVKDQWTSIASMQERRSTLGAAVLNDLLYAVGGFDGSTGLASVEAYSYKTNEWFFVAPMNTRRSSVGVGVVEGKLYAVGGYDGASRQCLSTVEQYNPATNEWIYVADMSTRRSGAGVGVLSGQLYATGGHDGPLVRKSVEVYDPGTNTWKQVADMNMCRRNAGVCAVNGLLYVVGGDDGSCNLASVEYYNPVTDKWTLLPTNMSTGRSYAGVAVIHKSL
1WZI , Knot 140 327 0.82 40 190 313 
MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLGSERSFQALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLI

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 \(c\).

\(|P_{f(3UJP_1)}(2) \setminus P_{f(5NKP_1)}(2)|=93\), \(|P_{f(5NKP_1)}(2) \setminus P_{f(3UJP_1)}(2)|=72\). 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 1:1010101000011000101100010100000001100101110110011100111001001110101001010011010010111001101001100111010011011100110111110110000101011101001110100100111010100100001011100001011000111010011100011100011100110001100101111010001010010011001000011011000010001000110101101110101001000011110110110001011001111100100
Pair \(Z_2\) Length of longest common subsequence
3UJP_1,5NKP_1 165 4
3UJP_1,1WZI_1 159 4
5NKP_1,1WZI_1 156 4

Newick tree

 
[
	3UJP_1:81.99,
	[
		1WZI_1:78,5NKP_1:78
	]:3.99
]

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 \((0.85)(0.8)(\frac{599 }{\log_{20} 599}-\frac{292}{\log_{20}292})=86.0\)
Status Protein1 Protein2 d d1/2
Query variables 3UJP_1 5NKP_1 106 99
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]