CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8IBU_1 5MAZ_1 2OPX_1 Letter Amino acid
4 0 5 H Histidine
27 8 34 L Leucine
24 2 22 K Lycine
7 0 15 M Methionine
18 5 16 F Phenylalanine
29 1 25 R Arginine
18 14 20 N Asparagine
8 2 21 P Proline
20 10 19 S Serine
28 5 21 D Aspartic acid
18 7 20 Q Glutamine
16 12 42 G Glycine
26 5 36 I Isoleucine
15 1 14 Y Tyrosine
29 11 59 A Alanine
7 0 3 C Cysteine
22 3 40 E Glutamic acid
18 11 20 T Threonine
4 1 7 W Tryptophan
23 16 40 V Valine 

8IBU_1|Chain A|Guanine nucleotide-binding protein G(q) subunit alpha|Homo sapiens (9606)
>5MAZ_1|Chains A, B, C, D|Fucose-binding lectin PA-IIL|Pseudomonas aeruginosa (strain UCBPP-PA14) (208963)
>2OPX_1|Chain A|Aldehyde dehydrogenase A|Escherichia coli BL21(DE3) (469008)
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 \(w=f(c)\)
8IBU , Knot 158 361 0.86 40 216 345 
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVNGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYNLV
5MAZ , Knot 56 114 0.77 34 83 110 
ATQGVFTLPANTQFGVTAFANSAGTQTVNVQVNNETVATFTGQSTNNAIIGSKVLNSGGGGKVQILVSVNGRSSDLVSAQVILANELNFALVGSEDSTDNDYNDAVVVINWPLG
2OPX , Knot 196 479 0.84 40 242 440 
MSVPVQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERATEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVALGGKAVEGKGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEEAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQS

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 \(c\).

\(|P_{f(8IBU_1)}(2) \setminus P_{f(5MAZ_1)}(2)|=160\), \(|P_{f(5MAZ_1)}(2) \setminus P_{f(8IBU_1)}(2)|=27\). 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 1:1100101000111000011000100000100001011111100010001100101001010000000000111000010011111011101010110010100100111111110011101011111001100011010100000001000110010010011010011000011000100011100010100101011011100000001100100101111110000000100110010011000110010111110000111001111000100011011000010010101100101001001100011010010101001001010001000010011000001110101000011
Pair \(Z_2\) Length of longest common subsequence
8IBU_1,5MAZ_1 187 3
8IBU_1,2OPX_1 154 4
5MAZ_1,2OPX_1 185 4

Newick tree

 
[
	5MAZ_1:97.75,
	[
		8IBU_1:77,2OPX_1:77
	]:20.75
]

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 \((0.85)(0.8)(\frac{475 }{\log_{20} 475}-\frac{114}{\log_{20}114})=107.\)
Status Protein1 Protein2 d d1/2
Query variables 8IBU_1 5MAZ_1 139 90
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]