CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5UJW_1 4EEO_1 5HUT_1 Letter Amino acid
4 4 5 C Cysteine
2 8 11 H Histidine
4 9 7 M Methionine
6 15 26 F Phenylalanine
21 17 38 S Serine
7 15 20 Y Tyrosine
21 20 40 V Valine
11 17 25 N Asparagine
19 21 31 G Glycine
25 16 38 I Isoleucine
18 11 36 K Lycine
19 9 34 E Glutamic acid
7 18 17 R Arginine
14 18 27 D Aspartic acid
13 17 15 Q Glutamine
26 24 45 L Leucine
5 19 20 P Proline
11 12 17 T Threonine
2 3 8 W Tryptophan
18 14 18 A Alanine 

5UJW_1|Chains A, B, C, D, E, F|Triosephosphate isomerase|Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (177416)
>4EEO_1|Chains A, B, C|Beta-1,4-galactosyltransferase 1|Homo sapiens (9606)
>5HUT_1|Chains A, B|Alpha,alpha-trehalose-phosphate synthase [UDP-forming]|Candida albicans (strain SC5314 / ATCC MYA-2876) (237561)
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 \(w=f(c)\)
5UJW , Knot 111 253 0.81 40 164 240 
MQKLIMGNWKMNGNSTSIKELCSGISQVQYDTSRVAIAVFPSSVYVKEVISQLPEKVGVGLQNITFYDDGAYTGEISARMLEDIGCDYLLIGHSERRSLFAESDEDVFKKLNKIIDTTITPVVCIGESLDDRQSGKLKQVLATQLSLILENLSVEQLAKVVIAYEPVWAIGTGVVASLEQIQETHQFIRSLLAKVDERLAKNIKIVYGGSLKAENAKDILSLPDVDGGLIGGASLKAAEFNEIINQANKICTE
4EEO , Knot 130 287 0.85 40 198 280 
ASMTGGQQMGRGSASLPACPEESPLLVGPMLIEFNMPVDLELVAKQNPNVKMGGRYAPRDCVSPHKVAIIIPFRNRQEHLKYWLYYLHPVLQRQQLDYGIYVINQAGDTIFNRAKLLNVGFQEALKDYDYTCFVFSDVDLIPMNDHNAYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKQQFLTINGFPNNYWGWGGEDDDIFNRLVFRGMSISRPNAVVGTTRHIRHSRDKKNEPNPQRFDRIAHTKETMLSDGLNSLTYQVLDVQRYPLYTQITVDIGTPS
5HUT , Knot 195 478 0.84 40 241 452 
MVQGKVLVVSNRIPVTIKRLDNGSYDYSMSSGGLVTALQGLKKTTEFQWYGWPGLEIPEDEQTKVNDELKSKFNCTAIFLSDTIADLHYNGFSNSILWPLFHYHPGEMNFDENAWAAYIEANKKFALEIVKQVNDDDMIWVHDYHLMLLPEMLRQEIGNKKKNIKIGFFLHTPFPSSEIYRILPVRKEILEGVLSCDLIGFHTYDYARHFISSVSRIVPNVSTLPNGIKYQGRSISIGAFPIGIDVDNFIDGLKKDSVVERIKQLKSKFKDVKVIVGVDRLDYIKGVPQKLHAFEVFLNENPEWIGKVVLVQVAVPSRGDVEEYQSLRSTVSELVGRINGEFGTVEFVPIHYLHKSIPFDELISLYNISDVCLVSSTRDGMNLVSYEYIACQQDRKGVLILSEFAGAAQSLNGALIVNPWNTEDLSEAIKESLTLPEEKREFNFKKLFTYISKYTSGFWGESFVKELYKCNPQKSLRD

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 \(c\).

\(|P_{f(5UJW_1)}(2) \setminus P_{f(4EEO_1)}(2)|=65\), \(|P_{f(4EEO_1)}(2) \setminus P_{f(5UJW_1)}(2)|=99\). 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 1:1001111010101000010010011001000000111111100101001100110011111001010001100101010110011000111100000011100000110010011000101110110010000010100111001011100101001101111001111110111101001000001100111010001100101101101010010011011010111111101011010011001001000
Pair \(Z_2\) Length of longest common subsequence
5UJW_1,4EEO_1 164 4
5UJW_1,5HUT_1 171 5
4EEO_1,5HUT_1 173 3

Newick tree

 
[
	5HUT_1:87.29,
	[
		5UJW_1:82,4EEO_1:82
	]:5.29
]

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 \((0.85)(0.8)(\frac{540 }{\log_{20} 540}-\frac{253}{\log_{20}253})=81.7\)
Status Protein1 Protein2 d d1/2
Query variables 5UJW_1 4EEO_1 109 97.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]