CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5BPQ_1 4KJL_1 5GMF_1 Letter Amino acid
2 14 24 A Alanine
5 13 39 D Aspartic acid
12 10 25 G Glycine
14 11 132 L Leucine
9 6 42 T Threonine
3 4 27 Y Tyrosine
5 9 35 R Arginine
7 5 70 N Asparagine
10 2 20 C Cysteine
15 12 36 P Proline
7 8 78 S Serine
12 12 40 E Glutamic acid
4 5 19 H Histidine
6 5 11 M Methionine
7 6 44 F Phenylalanine
8 11 37 V Valine
9 4 37 Q Glutamine
7 12 42 I Isoleucine
6 6 51 K Lycine
1 5 8 W Tryptophan 

5BPQ_1|Chains A, B, C, D|Frizzled-4|Homo sapiens (9606)
>4KJL_1|Chain A|Dihydrofolate reductase|Escherichia coli (83333)
>5GMF_1|Chains A, B, C, D|Toll-like receptor 7|Macaca mulatta (9544)
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 \(w=f(c)\)
5BPQ , Knot 74 149 0.82 40 122 145 
DTGERRCDPIRISMCQNLGYNVTKMPNLVGHELQTDAELQLTTFTPLIQYGCSSQLQFFLCSVYVPMCTEKINIPIGPCGGMCLSVKRRCEPVLKEFGFAWPESLNCSKFPPQNDHNHMCMEGPGDEEVPLPHKTPIQPGEGTLEVLFQ
4KJL , Knot 80 160 0.84 40 123 153 
MISLIAALAVDRVIGMENAMPWPPLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNAHSYCFEILERR
5GMF , Knot 298 817 0.81 40 279 684 
RSPWARWFPKTLPCDVTLDVSKNHVIVDCTDKHLTEIPGGIPTNTTNLTLTINHIPDISPASFHRLVHLVEIDFRCNCVPIRLGSKSNMCPRRLQIKPRSFSGLTYLKSLYLDGNQLLEIPQGLPPSLQLLSLEANNIFSIRKEQLTELANIEILYLGQNCYYRNPCYVSYSIEKDAFLNLTKLKVLSLKDNNVTTVPTVLPSTLTELYLYNNMIAEIQEDDFNNLNQLQILDLSGNCPRCYNAPFPCTPCKNNSPLQIPVNAFDALTELKVLRLHSNSLQHVPPRWFKNINNLQELDLSQNFLAKEIGDAKFLHFLPNLIQLDLSFNFELQVYRASMNLSQAFSSLKSLKILRIRGYVFKELKSFQLSPLHNLQNLEVLDLGTNFIKIANLSMFKQFKRLKVIDLSVNKISPSGDSSEVGFCSNARTSVESYEPQVLEQLYYFRYDKYARSCRFKNKEASFTSVQESCYKYGQTLDLSKNSIFFIKSSDFQHLSFLKCLNLSGNLISQTLNGSEFQPLAELRYLDFSNNRLDLLHSTAFEELRKLEVLDISSNSHYFQSEGITHMLNFTKNLKVLQKLMMNDNDISSSTSRTMESESLRTLEFRGNHLDVLWRDGDNRYLQLFKNLLKLEELDISKNSLSFLPSGVFDGMPPNLKNLSLAKNGLKSFIWEKLRYLKNLETLDLSHNQLTTVPERLSNCSRSLKNLILKNNQIRSLTKYFLQDAFQLRYLDLSSNKIQMIQKTSFPENVLNNLKMLLLHHNRFLCTCDAVWFVWWVQHTEVTIPYLATDVTCVGPGAHKGQSVISLDLYTCELDLTN

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 \(c\).

\(|P_{f(5BPQ_1)}(2) \setminus P_{f(4KJL_1)}(2)|=72\), \(|P_{f(4KJL_1)}(2) \setminus P_{f(5BPQ_1)}(2)|=73\). 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 1:00100000110101000110010011011100100010101001011100100001011100101110000101111101110101000001110011111100100001110000001010111000111100011011010101110
Pair \(Z_2\) Length of longest common subsequence
5BPQ_1,4KJL_1 145 3
5BPQ_1,5GMF_1 199 4
4KJL_1,5GMF_1 212 3

Newick tree

 
[
	5GMF_1:11.07,
	[
		5BPQ_1:72.5,4KJL_1:72.5
	]:38.57
]

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 \((0.85)(0.8)(\frac{309 }{\log_{20} 309}-\frac{149}{\log_{20}149})=49.1\)
Status Protein1 Protein2 d d1/2
Query variables 5BPQ_1 4KJL_1 64 61
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]