CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5FJQ_1 1DZH_1 2QFT_1 Letter Amino acid
5 35 17 K Lycine
5 26 13 F Phenylalanine
10 23 34 T Threonine
6 4 2 W Tryptophan
11 10 13 Y Tyrosine
10 28 24 V Valine
4 7 6 C Cysteine
8 14 12 Q Glutamine
15 18 37 G Glycine
8 5 8 H Histidine
16 31 46 A Alanine
14 23 26 D Aspartic acid
6 38 22 E Glutamic acid
1 12 14 M Methionine
11 21 17 P Proline
10 31 23 S Serine
12 22 21 R Arginine
9 22 18 N Asparagine
11 22 26 I Isoleucine
8 40 48 L Leucine 

5FJQ_1|Chains A, B, C|CARBOHYDRATE BINDING PROTEIN, PUTATIVE, CPB33A|CELLVIBRIO JAPONICUS (155077)
>1DZH_1|Chain A[auth I]|ANTITHROMBIN-III|HOMO SAPIENS (9606)
>2QFT_1|Chain A|3-phosphoshikimate 1-carboxyvinyltransferase|Escherichia coli (83333)
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 \(w=f(c)\)
5FJQ , Knot 87 180 0.83 40 150 176 
HGYVSSPKSRVIQCKENGIENPTHPACIAAKAAGNGGLYTPQEVAVGGVRDNHDYYIPDGRLCSANRANLFGMDLARNDWPATSVTPGAREFVWTNTAAHKTKYFRYYITPQGYDHSQPLRWSDLQLIHDSGPADQEWVSTHNVILPYRTGRHIIYSIWQRDWDRDAAEGFYQCIDVDFG
1DZH , Knot 183 432 0.85 40 227 404 
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFATTFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFAKLNCRLYRKAQKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRDDLYVSDAFHKAFLEVNEEGCEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMGRVANPCVK
2QFT , Knot 182 427 0.86 40 218 403 
MESLTLQPIARVDGTINLPGSKSVSNRALLLAALAHGKTVLTNLLDSDDVRHMLNALTALGVSYTLSADRTRCEIIGNGGPLHAEGALELFLGNAGTAMRSLAAALCLGSNDIVLTGEPRMKERPIGHLVDALRLGGAKITYLEQENYPPLRLQGGFTGGNVDVDGSVSSQFLTALLMTAPLAPEDTVIRIKGDLVSKPYIDITLNLMKTFGVEIENQHYQQFVVKGGQSYQSPGTYLVEGDASSASYFLAAAAIKGGTVKVTGIGRNSMQGDIRFADVLEKMGATICWGDDYISCTRGELNAIDMDMNHIPDAAMTIATAALFAKGTTTLRNIYNWRVKETDRLFAMATELRKVGAEVEEGHDYIRITPPEKLNFAEIATYNDHRMAMCFSLVALSDTPVTILDPKCTAKTFPDYFEQLARISQAA

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 \(c\).

\(|P_{f(5FJQ_1)}(2) \setminus P_{f(1DZH_1)}(2)|=60\), \(|P_{f(1DZH_1)}(2) \setminus P_{f(5FJQ_1)}(2)|=137\). 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 1:010100100011000001100100110111011101110010011111100000001101010010010111101100011100101110011100011000001000101010000011010010110001110001100001111000100110011000100011011000101011
Pair \(Z_2\) Length of longest common subsequence
5FJQ_1,1DZH_1 197 4
5FJQ_1,2QFT_1 184 4
1DZH_1,2QFT_1 163 4

Newick tree

 
[
	5FJQ_1:99.48,
	[
		2QFT_1:81.5,1DZH_1:81.5
	]:17.98
]

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 \((0.85)(0.8)(\frac{612 }{\log_{20} 612}-\frac{180}{\log_{20}180})=123.\)
Status Protein1 Protein2 d d1/2
Query variables 5FJQ_1 1DZH_1 156 110.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]