CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6UAY_1 5ITG_1 3VKS_1 Letter Amino acid
11 33 35 K Lycine
14 14 11 Y Tyrosine
7 27 39 R Arginine
13 35 47 E Glutamic acid
9 7 21 H Histidine
17 42 51 L Leucine
34 48 36 A Alanine
6 11 15 M Methionine
8 8 8 W Tryptophan
9 26 34 I Isoleucine
10 18 19 F Phenylalanine
19 26 24 S Serine
15 36 46 V Valine
16 18 24 N Asparagine
10 39 34 D Aspartic acid
2 4 11 C Cysteine
33 36 48 G Glycine
6 9 25 Q Glutamine
15 23 38 P Proline
7 24 25 T Threonine 

6UAY_1|Chains A, B|GLYCOSIDE HYDROLASE|Blastomyces gilchristii (1681229)
>5ITG_1|Chains A, B|Sorbitol dehydrogenase|Gluconobacter oxydans (442)
>3VKS_1|Chain A|Nitrite reductase|Nicotiana tabacum (4097)
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 \(w=f(c)\)
6UAY , Knot 116 261 0.82 40 167 248 
MGSSHHHHHHSSGLVPAGSHMADYYTIAANPGSGKRGLAYNNINLLTAFEGGPFSWSYNWEPRPGGYTAGIEYVPMLWGPRGYGSWNADAEAGIAAGSKNLLAFNEPDIASQANMSPEAAAAAYQKYMNPYAARARLGSPAVSNGAPPKGLGWMQGFLDVCAGNCKIDFLAVHWHGPSGNVDDFKRYVSEAIALGQKYGIGTVWVTEFEGQGDEEAQVNFLKEVLPWLDSNAGVERYASFFVDNLVKGGALTSVGKAYKTI
5ITG , Knot 197 484 0.83 40 240 453 
MITRETLKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHAPDWAIVGVGLTGSDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVDPAIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGGKAFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEIAKKLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAGHVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRFSNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKGGTYESSEPTYGDAEWKLAKADDFESSLKLPAFDGWRDLDTSELDQKVIVLRKIIREKGVKAAIP
3VKS , Knot 234 591 0.84 40 263 550 
MGHHHHHHHHHHSSGHIEGRHMFSKNAVKLHATPPSVAAPPTGAPEVAAERLEPRVEEKDGYWILKEQFRKGINPQEKVKIEKEPMKLFMENGIEELAKIPIEEIDQSKLTKDDIDVRLKWLGLFHRRKNQYGRFMMRLKLPNGVTTSAQTRYLASVIRKYGKEGCADITTRQNWQIRGVVLPDVPEILKGLAEVGLTSLQSGMDNVRNPVGNPLAGIDPEEIVDTRPYTNLLSQFITGNSRGNPAVSNLPRKWNPCVVGSHDLYEHPHINDLAYMPATKDGRFGFNLLVGGFFSAKRCDEAIPLDAWVPADDVVPVCRAILEAFRDLGFRGNRQKCRMMWLIDELGVEGFRAEVEKRMPQQQLERASPEDLVQKQWERRDYLGVHPQKQEGYSFIGLHIPVGRVQADDMDELARLADEYGSGEIRLTVEQNIIIPNIETSKIEALLKEPVLSTFSPDPPILMKGLVACTGNQFCGQAIIETKARSLKITEEVQRQVSLTKPVRMHWTGCPNTCAQVQVADIGFMGCLTRDKNGKTVEGADVFLGGRIGSDSHLGEVYKKAVPCDDLVPLVVDLLVNNFGAVPREREETED

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 \(c\).

\(|P_{f(6UAY_1)}(2) \setminus P_{f(5ITG_1)}(2)|=55\), \(|P_{f(5ITG_1)}(2) \setminus P_{f(6UAY_1)}(2)|=128\). 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 1:110000000000111111001100001110110100111000101101101111010001010111001110011111110101010101011111100011110010110010101011111000010101101011011100111101111101110101100010111101011010100100010011111000111011100101010001010110011111000111000101110011011110011010001
Pair \(Z_2\) Length of longest common subsequence
6UAY_1,5ITG_1 183 4
6UAY_1,3VKS_1 180 9
5ITG_1,3VKS_1 159 4

Newick tree

 
[
	6UAY_1:94.20,
	[
		3VKS_1:79.5,5ITG_1:79.5
	]:14.70
]

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 \((0.85)(0.8)(\frac{745 }{\log_{20} 745}-\frac{261}{\log_{20}261})=133.\)
Status Protein1 Protein2 d d1/2
Query variables 6UAY_1 5ITG_1 166 127
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]