CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3QQA_1 4QPR_1 1IUW_1 Letter Amino acid
17 5 18 I Isoleucine
7 10 19 T Threonine
9 3 16 Y Tyrosine
21 21 46 L Leucine
24 6 12 K Lycine
15 4 12 F Phenylalanine
3 5 38 R Arginine
2 0 5 C Cysteine
11 10 15 Q Glutamine
4 11 17 P Proline
1 2 6 W Tryptophan
10 7 28 V Valine
19 3 4 N Asparagine
12 8 9 H Histidine
4 4 6 M Methionine
10 11 34 G Glycine
15 7 21 S Serine
11 16 35 A Alanine
6 8 19 D Aspartic acid
15 8 34 E Glutamic acid 

3QQA_1|Chain A|CmeR|Campylobacter jejuni (197)
>4QPR_1|Chain A|Sensor protein KdpD|Escherichia coli (83333)
>1IUW_1|Chain A|P-HYDROXYBENZOATE HYDROXYLASE|Pseudomonas aeruginosa (208964)
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 \(w=f(c)\)
3QQA , Knot 94 216 0.78 40 137 206 
HHHHHHMNSNRTPSQKVLARQEKIKAVALELFLTKGYQETSLSDIIKLSGGSYSNIYDGFKSKEGLFFEILDDICKKHFHLIYSKTQEIKNGTLKEILTSFGLAFIEIFNQPEAVAFGKIIYSQVYDKDRHLANWIENNQQNFSYNILMGFFKQQNNSYMKKNAEKLAVLFCTMLKEPYHHLNVLINAPLKNKKEQKEHVEFVVNVFLNGINSSKA
4QPR , Knot 71 149 0.79 38 114 143 
GAMDLYEMSKALAVGRSPQDIAATSEQFIASTFHARSQVLLPDDNGKLQPLTHPQGMTPWDDAIAQWSFDKGLPAGAGTDTLPGVPYQILPLKSGEKTYGLVVVEPGNLRQLMIPEQQRLLETFTLLVANALERLTKLAAALEHHHHHH
1IUW , Knot 163 394 0.82 40 216 373 
MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLSEKVEDWSDERFWTELKARLPSEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYEEIE

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 \(c\).

\(|P_{f(3QQA_1)}(2) \setminus P_{f(4QPR_1)}(2)|=86\), \(|P_{f(4QPR_1)}(2) \setminus P_{f(3QQA_1)}(2)|=63\). 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 1:000000100000100011100001011110111001000001001101011000010011000011110110010000101100000010010100110011111101100101111101100010000001101100000010001111110000000100010011111001100100010111011100000000010111011101100001
Pair \(Z_2\) Length of longest common subsequence
3QQA_1,4QPR_1 149 6
3QQA_1,1IUW_1 207 4
4QPR_1,1IUW_1 176 4

Newick tree

 
[
	1IUW_1:10.24,
	[
		3QQA_1:74.5,4QPR_1:74.5
	]:27.74
]

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 \((0.85)(0.8)(\frac{365 }{\log_{20} 365}-\frac{149}{\log_{20}149})=65.3\)
Status Protein1 Protein2 d d1/2
Query variables 3QQA_1 4QPR_1 79 68
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]