CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
8FJF_1 1MUC_1 3KEK_1 Letter Amino acid
3 11 6 N Asparagine
0 3 3 W Tryptophan
5 5 9 Y Tyrosine
15 45 9 A Alanine
8 21 16 D Aspartic acid
0 2 0 C Cysteine
0 16 2 Q Glutamine
12 34 16 G Glycine
0 28 3 R Arginine
2 8 9 H Histidine
6 15 12 P Proline
9 18 12 S Serine
5 20 10 T Threonine
15 20 7 V Valine
16 24 5 E Glutamic acid
5 30 7 I Isoleucine
6 45 13 L Leucine
21 13 10 K Lycine
0 7 5 M Methionine
6 8 13 F Phenylalanine 

8FJF_1|Chain A|H10|synthetic construct (32630)
>1MUC_1|Chains A, B|MUCONATE LACTONIZING ENZYME|Pseudomonas putida (303)
>3KEK_1|Chains A, B|Collagenase 3|Homo sapiens (9606)
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 \(w=f(c)\)
8FJF , Knot 45 134 0.54 30 62 89 
SGSKYVVIDGEGNEYEFTDLKEAAAKAKELKKKYGFASISVPVEPDEVAVVDGKGNEHTFTDIKKAVEKAKELAKETGFASISVPVEPDEYLVIDGKGNEHKFTDLKEAVAKAKELKKKYGFASVSVPVPAGSG
1MUC , Knot 152 373 0.80 40 195 346 
MTSALIERIDAIIVDLPTIRPHKLAMHTMQQQTLVVLRVRCSDGVEGIGEATTIGGLAYGYESPEGIKANIDAHLAPALIGLAADNINAAMLKLDKLAKGNTFAKSGIESALLDAQGKRLGLPVSELLGGRVRDSLEVAWTLASGDTARDIAEARHMLEIRRHRVFKLKIGANPVEQDLKHVVTIKRELGDSASVRVDVNQYWDESQAIRACQVLGDNGIDLIEQPISRINRGGQVRLNQRTPAPIMADESIESVEDAFSLAADGAASIFALKIAKNGGPRAVLRTAQIAEAAGIGLYGGTMLEGSIGTLASAHAFLTLRQLTWGTELFGPLLLTEEIVNEPPQYRDFQLHIPRTPGLGLTLDEQRLARFARR
3KEK , Knot 80 167 0.81 38 125 162 
YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGD

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 \(c\).

\(|P_{f(8FJF_1)}(2) \setminus P_{f(1MUC_1)}(2)|=19\), \(|P_{f(1MUC_1)}(2) \setminus P_{f(8FJF_1)}(2)|=152\). 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 1:01000111010100001001001110100100001110101110100111101010000100100110010011000111010111010001110101000010010011101001000011101011111101
Pair \(Z_2\) Length of longest common subsequence
8FJF_1,1MUC_1 171 3
8FJF_1,3KEK_1 133 4
1MUC_1,3KEK_1 178 4

Newick tree

 
[
	1MUC_1:93.16,
	[
		8FJF_1:66.5,3KEK_1:66.5
	]:26.66
]

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 \((0.85)(0.8)(\frac{507 }{\log_{20} 507}-\frac{134}{\log_{20}134})=110.\)
Status Protein1 Protein2 d d1/2
Query variables 8FJF_1 1MUC_1 140 87
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: