CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5WIZ_1 7YVT_1 4TXO_1 Letter Amino acid
27 12 6 S Serine
4 5 3 W Tryptophan
21 9 9 V Valine
39 40 32 A Alanine
17 15 12 D Aspartic acid
5 7 3 M Methionine
14 21 14 P Proline
6 3 5 N Asparagine
10 12 5 Q Glutamine
29 29 12 G Glycine
7 19 1 H Histidine
12 13 6 F Phenylalanine
25 15 11 T Threonine
26 14 7 R Arginine
2 4 3 C Cysteine
16 13 10 E Glutamic acid
26 14 7 I Isoleucine
35 34 21 L Leucine
7 7 16 K Lycine
5 9 1 Y Tyrosine 

5WIZ_1|Chains A, B[auth G]|Phosphotriesterase|Brevundimonas diminuta (293)
>7YVT_1|Chains A, B, C|S-formylglutathione hydrolase|Variovorax sp. (1871043)
>4TXO_1|Chains A, C, E, G|Thiol:disulfide interchange protein TlpA|Bradyrhizobium diazoefficiens USDA 110 (224911)
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 \(w=f(c)\)
5WIZ , Knot 143 333 0.83 40 189 308 
MGDRINTVRGPITISEAGFTLTHEHICGSSAGFLRAWPEFFGSRKALAEKAVRGLRRARAAGVRTIVDVSTFDLGRDVSLLAEVSRAADVHIVAATGLWLDPPLSMRLRSVEELTQFFLREIQYGIEDTGIRAGIIKVATTGKVTPFQELVLRAAARASLATGVPVTTHTAASQRGGEQQAAILESEGLSPSRVCIGHSDATDDLSYLTALAARGYLIGLDSIPHSAIGLEDNASASAHLGIRSWQTRALLIKALIDQGYTKQILVSNDWLFGISSYVTNIMDVMDSGNPDGMAFIPLRVIPFLREKGIPQETLAGITVTNPARFLSPTLRAS
7YVT , Knot 129 295 0.83 40 188 287 
MTDSIKTLSAHRSFGGVQHFHEHASREIGLPMRFAAYLPPQAEHGKVPALLYLAGLTCNEETFMVKAGAQRLAAELGIALIAPDTSPRGAHIDGESTSWDFGVGAGFYLDATAAPWAPNWRMESYLVDELLPLLAKTLPIDGDRIGVFGHSMGGHGALTLALRHPGLFKSLSAFAPICAPTQCPWGHKAFTGYLGADTTRWIEHDATVLMQHQPVAPYPAGILIDQGLADKFLAEQLHPHLLEDACRAIGQPLTLRRHEGYDHGYYFVQSFMADHLAHHAQILNGAIGRPAARQP
4TXO , Knot 83 184 0.78 40 122 174 
APTGDPACRAAVATAQKIAPLAHGEVAALTMASAPLKLPDLAFEDADGKPKKLSDFRGKTLLVNLWATWCVPSRKEMPALDELQGKLSGPNFEVVAINIDTRDPEKPKTFLKEANLTRLGYFNDQKAKVFQDLKAIGRALGMPTSVLVDPQGCEIATIAGPAEWASEDALKLIRAATGKAAAAL

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 \(c\).

\(|P_{f(5WIZ_1)}(2) \setminus P_{f(7YVT_1)}(2)|=79\), \(|P_{f(7YVT_1)}(2) \setminus P_{f(5WIZ_1)}(2)|=78\). 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 1:110010010111010011101000010100111101110111000111001101100101111001101001011001011101001101011110111101110101001001001110010011000110111101100101011001110111010110111100001100011000111100011010010110001000100101111010111100110011110001010101110010001111011100100001110001111100010011011001010111111101111100011100011110100110110101010
Pair \(Z_2\) Length of longest common subsequence
5WIZ_1,7YVT_1 157 5
5WIZ_1,4TXO_1 153 4
7YVT_1,4TXO_1 166 4

Newick tree

 
[
	7YVT_1:82.15,
	[
		5WIZ_1:76.5,4TXO_1:76.5
	]:5.65
]

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 \((0.85)(0.8)(\frac{628 }{\log_{20} 628}-\frac{295}{\log_{20}295})=92.9\)
Status Protein1 Protein2 d d1/2
Query variables 5WIZ_1 7YVT_1 115 109
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]