CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2LQT_1 7FUO_1 5UYH_1 Letter Amino acid
6 18 14 D Aspartic acid
5 32 22 E Glutamic acid
4 5 4 M Methionine
3 23 12 F Phenylalanine
1 4 5 W Tryptophan
2 14 16 G Glycine
3 43 18 K Lycine
4 18 22 V Valine
4 14 34 A Alanine
7 18 14 N Asparagine
4 14 17 T Threonine
4 11 11 Y Tyrosine
6 28 22 S Serine
12 20 13 R Arginine
4 10 0 C Cysteine
2 12 13 Q Glutamine
0 8 15 H Histidine
3 18 30 I Isoleucine
5 41 21 L Leucine
6 11 20 P Proline 

2LQT_1|Chain A|Coiled-coil-helix-coiled-coil-helix domain-containing protein 7|Homo sapiens (9606)
>7FUO_1|Chain A|Cyclic GMP-AMP synthase|Homo sapiens (9606)
>5UYH_1|Chain A|Periplasmic chelated iron-binding protein YfeA|Yersinia pestis (632)
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 \(w=f(c)\)
2LQT , Knot 47 85 0.82 38 71 83 
MPSVTQRLRDPDINPCLSESDASTRCLDENNYDRERCSTYFLRYKNCRRFWNSIVMQRRKNGVKPFMPTAAERDEILRAVGNMPY
7FUO , Knot 149 362 0.80 40 204 345 
GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
5UYH , Knot 134 323 0.80 38 186 303 
MIERLNSPFLRAAALFTIVAFSSLISTAALAENNPSDTAKKFKVVTTFTIIQDIAQNIAGDVAVVESITKPGAEIHDYQPTPRDIVKAQSADLILWNGMNLERWFEKFFESIKDVPSAVVTAGITPLPIREGPYSGIANPHAWMSPSNALIYIENIRKALVEHDPAHAETYNRNAQAYAEKIKALDAPLRERLSRIPAEQRWLVTSEGAFSYLAKDYGFKEVYLWPINAEQQGIPQQVRHVIDIIRENKIPVVFSESTISDKPAKQVSKETGAQYGGVLYVDSLSGEKGPVPTYISLINMTVDTIAKGFGQLEHHHHHHHHHH

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 \(c\).

\(|P_{f(2LQT_1)}(2) \setminus P_{f(7FUO_1)}(2)|=27\), \(|P_{f(7FUO_1)}(2) \setminus P_{f(2LQT_1)}(2)|=160\). 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 1:1101000100101010100001000010000000000000110000000110011100000110111101100001101110110
Pair \(Z_2\) Length of longest common subsequence
2LQT_1,7FUO_1 187 4
2LQT_1,5UYH_1 171 3
7FUO_1,5UYH_1 170 5

Newick tree

 
[
	2LQT_1:91.06,
	[
		5UYH_1:85,7FUO_1:85
	]:6.06
]

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 \((0.85)(0.8)(\frac{447 }{\log_{20} 447}-\frac{85}{\log_{20}85})=110.\)
Status Protein1 Protein2 d d1/2
Query variables 2LQT_1 7FUO_1 138 84.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: