CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5WBA_1 6XSZ_1 1DEL_1 Letter Amino acid
5 41 12 E Glutamic acid
10 45 15 N Asparagine
0 1 2 C Cysteine
7 20 6 Q Glutamine
9 29 18 V Valine
5 16 10 R Arginine
3 16 6 P Proline
6 9 3 W Tryptophan
4 32 17 I Isoleucine
8 36 21 L Leucine
20 39 15 T Threonine
23 29 17 A Alanine
7 35 22 D Aspartic acid
2 13 3 H Histidine
2 21 13 F Phenylalanine
12 37 11 S Serine
6 27 11 Y Tyrosine
21 38 15 G Glycine
6 34 17 K Lycine
3 13 7 M Methionine 

5WBA_1|Chain A|Streptavidin|Streptomyces avidinii (1895)
>6XSZ_1|Chains A, B, C, D|ZmpC Glycopeptidase|Clostridium perfringens (1502)
>1DEL_1|Chains A, B|DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE|Enterobacteria phage T4 (10665)
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 \(w=f(c)\)
5WBA , Knot 74 159 0.78 38 109 153 
MASMTGGQQMGRDEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ
6XSZ , Knot 211 531 0.83 40 252 504 
MGSSHHHHHHSSGLVPRGSHMASVIELEMRGNSVQEANYRKMWGFQDWQVTGLSALAGDKITVYVDVEEGEPTPTLLYRQTMTQHGGAKTFQLQNGKNEIVIPELDKTSNGISEGTIQGGELFFTNYNSDSQTRAPKIRIEGAKEYPVFVLGESDEDKVIKELEAYVEKIEKEPETTPDIFAVSSNKSLSLTQATYALEWYKNNNKTPKYTAESWDKIVENAMDFWGYDNSSELNSDFNFRIMPMVKNLTGGAFMNAHSGVIGIRPGNQNCIVGADMGWGTMHELGHNFDTSGRTIAEVTNNIMPLYFESLNRTQTRITDQNIWENNTYPKVGLDDYSNNKLYNTSDSTHLAQLAPLWQLYLYDNTFYGKFEQQFRANNYGNKTREDIYKSWVVAASNAMQLDLTEFFARHGIRINDEVAQEISSKYEKPDKKIYYLNDLAINYEGNGFTENAQVDIKTTNSDGKVKLVFSINEEDKDNLLGYEIRKDGKYIGFTSKDSFVDTSSNLEDDAVYTVTPYDIKLNTLNAIEVD
1DEL , Knot 109 241 0.82 40 170 236 
MKLIFLSGVKRSGKDTTADFIMSNYSAVKYQLAGPIKDALAYAWGVFAANTDYPCLTRKEFEGIDYDRETNLNLTKLEVITIMEQAFCYLNGKSPIKGVFVFDDEGKESVNFVAFNKITDVINNIEDQWSVRRLMQALGTDLIVNNFDRMYWVKLFALDYLDKFNSGYDYYIVPDTRQDHEMDAARAMGATVIHVVRPGQKSNDTHITEAGLPIRDGDLVITNDGSLEELFSKIKNTLKVL

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 \(c\).

\(|P_{f(5WBA_1)}(2) \setminus P_{f(6XSZ_1)}(2)|=24\), \(|P_{f(6XSZ_1)}(2) \setminus P_{f(5WBA_1)}(2)|=167\). 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 1:110101100110001110101000110011101110111010000111010000110100001110010101111011100000010010010100111101010001110010001011000111000100101011010110011100101101100
Pair \(Z_2\) Length of longest common subsequence
5WBA_1,6XSZ_1 191 4
5WBA_1,1DEL_1 167 3
6XSZ_1,1DEL_1 162 3

Newick tree

 
[
	5WBA_1:92.41,
	[
		1DEL_1:81,6XSZ_1:81
	]:11.41
]

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 \((0.85)(0.8)(\frac{690 }{\log_{20} 690}-\frac{159}{\log_{20}159})=151.\)
Status Protein1 Protein2 d d1/2
Query variables 5WBA_1 6XSZ_1 191 122
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]