CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5QGQ_1 1NZC_1 8ROQ_1 Letter Amino acid
9 6 39 I Isoleucine
3 3 31 M Methionine
14 11 57 P Proline
4 10 64 S Serine
8 7 63 Y Tyrosine
13 13 56 D Aspartic acid
9 3 12 H Histidine
23 18 66 L Leucine
12 15 25 K Lycine
9 15 49 F Phenylalanine
11 6 73 T Threonine
0 5 17 W Tryptophan
10 7 44 R Arginine
11 14 62 G Glycine
18 16 53 V Valine
6 12 80 N Asparagine
4 0 5 C Cysteine
11 18 33 E Glutamic acid
14 14 66 A Alanine
7 4 42 Q Glutamine 

5QGQ_1|Chain A|Peroxisomal coenzyme A diphosphatase NUDT7|Homo sapiens (9606)
>1NZC_1|Chains A, B, C, D|dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase|Streptococcus suis (1307)
>8ROQ_1|Chains A, B, C, D, E, F, G, H, I, J, K, L|Hexon protein|Fowl aviadenovirus C (190063)
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 \(w=f(c)\)
5QGQ , Knot 92 196 0.82 38 147 187 
SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
1NZC , Knot 94 197 0.84 38 149 194 
MTENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL
8ROQ , Knot 345 937 0.84 40 309 847 
MAALTPDLTTATPRLQYFHIAGPGTREYLSEDLQQFISATGSYFDLKNKFRQTVVAPTRNVTTEKAQRLQIRFYPIQTDDTSTGYRVRYNINVGDGWVLDMGSTYFDIKGILDRGPSFKPYCGTAYNPLAPKESMFNNWSETAPGQNVSASGQLSNVYTNTSTTKDTTAAQVTKISGVFPNPNQGPGINPLRQVENANTGVLGRFAKSQYNYAYGAYVKPVAADGSQSLTQTPYWIMNNAGTEYLGAVAVEDYTNSLSYPDTMIVPPPEDYDDYNIGTTRALRPNYIGFRDNFINLLYHDSGVCSGTLNSERSGMNVVVELPDRNTELSYQYMLADMMSRHHYFALWNQAVDQYDPEVRVFSNDGYEEGAPSYAFNPEAVGAGEGYGPDLSQIKLYTNNTAANDKNTAVTNATTNFYFGTVPSYEIDISATQRRNFIMANIAEYLPDRYKFSISGFDATSVAPTTYEYMNKRVPLTNVVDMFTNVGARWSIDQMDNVNPFNHHRNWGLKYRSQLLGNSRYVNFHIQVPQKFFAIKNLLLLSGSYTYEWVLRKDPNMILQSSLGNDLRADGASIIYNEVNLMANFMPMDHNTSNQLELMLRNATNDQTFVDYLGAKNALYSVPAGSTALTINIPARTWEGMRGWSFTRIKAAETPQLGAQYDVNFKYSGSIAYSDGGFYLSHTFRNMSILFDTSINWPGNDRLLTPNMFEIKRSVALDTEGFTMSQCDITKDWYLIQMATNYNFVYNGYRFWPDRQYFHYDFLRNFDPMTRQGPNFALPGLFDLVSYTPTTDNSGEQPSQEAVRNNSGFIAPRSWPVWSAHQGESWPANWPYPLCGQQAIQPGQVLSYKKFLCDNYLWTIPFSSDFMYMGELTDLGQNPMYTNNSHSMVINFELDPMDDPTYVYMLYGVFDTVRVNQPERNVLAMAYFRTPFATGNAV

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 \(c\).

\(|P_{f(5QGQ_1)}(2) \setminus P_{f(1NZC_1)}(2)|=76\), \(|P_{f(1NZC_1)}(2) \setminus P_{f(5QGQ_1)}(2)|=78\). 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 1:0110010101000011100001100000111111100101011101000010011101011110001001001101100100011101001011001110110000110111111000101010110100111111101101010000010011001100110000100110001011010111111111100010
Pair \(Z_2\) Length of longest common subsequence
5QGQ_1,1NZC_1 154 4
5QGQ_1,8ROQ_1 190 3
1NZC_1,8ROQ_1 202 4

Newick tree

 
[
	8ROQ_1:10.12,
	[
		5QGQ_1:77,1NZC_1:77
	]:27.12
]

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 \((0.85)(0.8)(\frac{393 }{\log_{20} 393}-\frac{196}{\log_{20}196})=58.3\)
Status Protein1 Protein2 d d1/2
Query variables 5QGQ_1 1NZC_1 73 72
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]