CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5NPL_1 5FLL_1 5KWB_1 Letter Amino acid
15 15 19 I Isoleucine
14 18 16 K Lycine
1 5 6 W Tryptophan
6 7 19 Y Tyrosine
10 19 21 G Glycine
6 8 23 F Phenylalanine
20 18 23 V Valine
25 16 11 A Alanine
3 14 6 H Histidine
9 10 22 T Threonine
19 29 8 E Glutamic acid
4 6 37 N Asparagine
13 16 23 D Aspartic acid
5 3 24 C Cysteine
10 8 7 Q Glutamine
12 16 26 L Leucine
5 9 0 M Methionine
10 11 18 P Proline
13 14 13 R Arginine
8 18 49 S Serine 

5NPL_1|Chains A, B, C|Similar to tr|Q8YYT1|Q8YYT1|Microcystis aeruginosa PCC 7806 (267872)
>5FLL_1|Chains A, B|6-CARBOXYHEXANOATE-COA LIGASE|BACILLUS SUBTILIS (1423)
>5KWB_1|Chain A|Spike glycoprotein|Human coronavirus HKU1 (isolate N1) (443239)
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 \(w=f(c)\)
5NPL , Knot 97 208 0.83 40 148 202 
GPMVLQAQEIMTQNVVTIRGSATVADAVKLMKEKKLRGLIVEPRHEQDPYGIVTETDIVYKVAAFGHDPKTMRVYEIMAKPCVVVNPELGVEYVARLFAQTRIRRAPVIQGKTLLGIISVSDILFKSDFVEKPKRLFIEDEIEAAREDARAICAAKGETSPDCAAAWDVVEELQAEASHQRAKKQGSNSFQAYCEANPDALECRIYDD
5FLL , Knot 115 260 0.82 40 169 247 
GAMEEETFYSVRMRASMNGSHEDGGKHISGGERLIPFHEMKHTVNALLEKGLSHSRGKPDFMQIQFEEVHESIKTIQPLPVHTNEVSCPEEGQKLARLLLEKEGVSRDVIEKAYEQIPEWSDVRGAVLFDIHTGKRMDQTKEKGVRVSRMDWPDANFEKWALHSHVPAHSRIKEALALASKVSRHPAVVAELCWSDDPDYITGYVAGKKMGYQRITAMKEYGTEEGCRVFFIDGSNDVNTYIHDLEKQPILIEWEEDHDS
5KWB , Knot 157 371 0.83 38 198 352 
SGFTVKPVATVHRRIPDLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTDSFSCNNFDESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLYYSLPAINVTINNYNPSSWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCKSHKPPSASCPIGTNYRSCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHCAGFGVDEEKCGVLDGSYNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCSNDLLQPNTEVFTDVCVDYDLYGITGQGIFKEVSAVYYNSWQNLLYDSNGNIIGFKDFVTNKTYNIFPCYAG

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 \(c\).

\(|P_{f(5NPL_1)}(2) \setminus P_{f(5FLL_1)}(2)|=72\), \(|P_{f(5FLL_1)}(2) \setminus P_{f(5NPL_1)}(2)|=93\). 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 1:1111101001100011010101011011011000010111101000001011100001100111110010010100111010111010111001101110001001111010011111010011100011001001110001011000101101101000100111101100101010000100010001010001010110001000
Pair \(Z_2\) Length of longest common subsequence
5NPL_1,5FLL_1 165 3
5NPL_1,5KWB_1 188 3
5FLL_1,5KWB_1 195 3

Newick tree

 
[
	5KWB_1:99.79,
	[
		5NPL_1:82.5,5FLL_1:82.5
	]:17.29
]

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 \((0.85)(0.8)(\frac{468 }{\log_{20} 468}-\frac{208}{\log_{20}208})=75.6\)
Status Protein1 Protein2 d d1/2
Query variables 5NPL_1 5FLL_1 95 86
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]