CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7TIM_1 6ZLH_1 3FBI_1 Letter Amino acid
26 54 2 V Valine
25 47 7 A Alanine
2 0 1 C Cysteine
17 13 6 E Glutamic acid
3 10 0 H Histidine
11 20 3 F Phenylalanine
3 3 1 W Tryptophan
6 14 5 Y Tyrosine
8 15 1 R Arginine
15 12 2 D Aspartic acid
15 34 3 I Isoleucine
21 18 8 K Lycine
0 17 2 M Methionine
7 18 12 P Proline
12 25 3 T Threonine
12 10 7 N Asparagine
7 9 4 Q Glutamine
22 46 4 G Glycine
19 55 5 L Leucine
16 18 8 S Serine 

7TIM_1|Chains A, B|TRIOSEPHOSPHATE ISOMERASE|Saccharomyces cerevisiae (4932)
>6ZLH_1|Chains A, B, C|Proton/glutamate symporter, SDF family|Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (69014)
>3FBI_1|Chains A, C|Mediator of RNA polymerase II transcription subunit 7|Saccharomyces cerevisiae (4932)
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 \(w=f(c)\)
7TIM , Knot 109 247 0.81 38 155 236 
ARTFFVGGNFKLNGSKQSIKEIVERLNTASIPENVEVVICPPATYLDYSVSLVKKPQVTVGAQNAYLKASGAFTGENSVDQIKDVGAKWVILGHSERRSYFHEDDKFIADKTKFALGQGVGVILCIGETLEEKKAGKTLDVVERQLNAVLEEVKDWTNVVVAYEPVWAIGTGLAATPEDAQDIHASIRKFLASKLGDKAASELRILYGGSANGSNAVTFKDKADVDGFLVGGASLKPEFVDIINSRN
6ZLH , Knot 166 438 0.76 38 197 394 
MGKSLLRRYLDYPVLWKILWGLVLGAVFGLIAGHFGYAGAVKTYIKPFGDLFVRLLKMLVMPIVLASLVVGAASISPARLGRVGVKIVVYYLATSAMAVFFGLIVGRLFNVGANVNLGSGTGKAIEAQPPSLVQTLLNIVPTNPFASLAKGEVLPVIFFAIILGIAITYLMNRNEERVRKSAETLLRVFDGLAEAMYLIVGGVMQYAPIGVFALIAYVMAEQGVRVVGPLAKVVGAVYTGLFLQIVITYFILLKVFGIDPIKFIRKAKDAMITAFVTRSSSGTLPVTMRVAEEEMGVDKGIFSFTLPLGATINMDGTALYQGVTVLFVANAIGHPLTLGQQLVVVLTAVLASIGTAGVPGAGAIMLAMVLQSVGLDLTPGSPVALAYAMILGIDAILDMGRTMVNVTGDLAGTVIVAKTEKELDESKWISHHHHHHHH
3FBI , Knot 45 84 0.79 38 71 79 
MASNDPGNEVSSLYPPPPPYVKFFTQSNLEKLPKYKEKKAASAKQTAPNNSNGGSEEEITCALDYLIPPPMPKNQQYRAFGSIW

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 \(c\).

\(|P_{f(7TIM_1)}(2) \setminus P_{f(6ZLH_1)}(2)|=54\), \(|P_{f(6ZLH_1)}(2) \setminus P_{f(7TIM_1)}(2)|=96\). 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 1:1001111101010100001001100100101100101110111001000101100101011100101010111010001001001110111110000000100000111000011110111111011001000011001011000101110010010011110011111101111010010010101001110011001100101101101010011010001010111111101010110110000
Pair \(Z_2\) Length of longest common subsequence
7TIM_1,6ZLH_1 150 4
7TIM_1,3FBI_1 150 4
6ZLH_1,3FBI_1 182 3

Newick tree

 
[
	3FBI_1:85.99,
	[
		7TIM_1:75,6ZLH_1:75
	]:10.99
]

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 \((0.85)(0.8)(\frac{685 }{\log_{20} 685}-\frac{247}{\log_{20}247})=122.\)
Status Protein1 Protein2 d d1/2
Query variables 7TIM_1 6ZLH_1 143 113.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]