CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2YBB_1 3CIR_1 2HTB_1 Letter Amino acid
9 23 13 N Asparagine
6 10 5 C Cysteine
49 66 22 G Glycine
21 23 12 I Isoleucine
31 22 18 P Proline
18 17 5 Y Tyrosine
23 41 27 V Valine
33 62 26 A Alanine
21 20 16 S Serine
22 35 19 T Threonine
17 35 19 D Aspartic acid
10 22 11 Q Glutamine
8 7 7 W Tryptophan
30 38 13 R Arginine
36 44 16 E Glutamic acid
9 21 19 H Histidine
43 48 28 L Leucine
23 27 14 K Lycine
13 21 6 M Methionine
16 20 13 F Phenylalanine 

2YBB_1|Chain A[auth 1]|NADH-QUINONE OXIDOREDUCTASE SUBUNIT 1|THERMUS THERMOPHILUS (300852)
>3CIR_1|Chains A, E[auth M]|Fumarate reductase flavoprotein subunit|Escherichia coli (562)
>2HTB_1|Chains A, B, C, D|Putative enzyme related to aldose 1-epimerase|Salmonella typhimurium (90371)
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 \(w=f(c)\)
2YBB , Knot 184 438 0.85 40 230 414 
MTGPILSGLDPRFERTLYAHVGKEGSWTLDYYLRHGGYETAKRVLKEKTPDEVIEEVKRSGLRGRGGAGFPTGLKWSFMPKDDGKQHYLICNADESEPGSFKDRYILEDVPHLLIEGMILAGYAIRATVGYIYVRGEYRRAADRLEQAIKEARARGYLGKNLFGTDFSFDLHVHRGAGAYICGEETALMNSLEGLRANPRLKPPFPAQSGLWGKPTTINNVETLASVVPIMERGADWFAQMGTEQSKGMKLYQISGPVKRPGVYELPMGTTFRELIYEWAGGPLEPIQAIIPGGSSTPPLPFTEEVLDTPMSYEHLQAKGSMLGTGGVILIPERVSMVDAMWNLTRFYAHESCGKCTPCREGVAGFMVNLFAKIGTGQGEEKDVENLEALLPLIEGRSFCPLADAAVWPVKGSLRHFKDQYLALAREKRPVPRPSLWR
3CIR , Knot 240 602 0.85 40 275 565 
MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDHDSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGMKIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGTLVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPAGLPGSGILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWRKGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMGGIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGNGNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKLAELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGCTERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPAKRVYGGEADAADKAEAANKKEKANG
2HTB , Knot 139 309 0.86 40 195 300 
MRGSHHHHHHGMASHMINKIFALPVIEQLTPVLSRRQLDDLDLIVVDHPQVKASFALQGAHLLSWKPVGEEEVLWLSNNTPFKTGVALRGGVPICWPWFGPAAQQGLPSHGFARNLPWALKAHNEDDNGVMLTFELQSSEATRKYWPHDFTLLARFKVGKTCEIELEAHGEFATTSALHSYFNVGDIANVKVSGLGDRFIDKVNDAKEGVLTDGIQTFPDRTDRVYLNPEACSVIHDATLNRTIDVVHHHHLNVVGWNPGPALSVSMGDMPDDGYKTFVCVETVYATAPQQATEEKPSRLAQTICVAKR

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 \(c\).

\(|P_{f(2YBB_1)}(2) \setminus P_{f(3CIR_1)}(2)|=53\), \(|P_{f(3CIR_1)}(2) \setminus P_{f(2YBB_1)}(2)|=98\). 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 1:101111011010100010101100101010001001100010011000010011001000110101111110110101110001000011001000011010000110011011101111110110101101010100001100100110010101011001110010101010011110101000111001011010101011111001111010010010011011111001101110110000011010010111001110011110010011001111110110111111000111110001100110000101010111011111110010110111010010100001000100011111110111011010100001001011111101001011101111110101001000011110000111010110
Pair \(Z_2\) Length of longest common subsequence
2YBB_1,3CIR_1 151 4
2YBB_1,2HTB_1 163 4
3CIR_1,2HTB_1 172 4

Newick tree

 
[
	2HTB_1:86.36,
	[
		2YBB_1:75.5,3CIR_1:75.5
	]:10.86
]

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 \((0.85)(0.8)(\frac{1040 }{\log_{20} 1040}-\frac{438}{\log_{20}438})=158.\)
Status Protein1 Protein2 d d1/2
Query variables 2YBB_1 3CIR_1 208 177.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]