CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3CWC_1 4XMA_1 2LLT_1 Letter Amino acid
7 35 2 Y Tyrosine
56 31 7 A Alanine
23 34 12 E Glutamic acid
22 42 4 T Threonine
12 49 9 K Lycine
7 9 2 M Methionine
6 29 5 F Phenylalanine
12 20 0 P Proline
19 21 0 R Arginine
24 41 8 D Aspartic acid
11 25 3 Q Glutamine
18 73 5 S Serine
5 1 1 C Cysteine
29 46 1 I Isoleucine
36 51 11 L Leucine
2 8 1 W Tryptophan
28 35 9 V Valine
10 45 5 N Asparagine
45 53 6 G Glycine
11 10 2 H Histidine 

3CWC_1|Chains A, B|Putative glycerate kinase 2|Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (99287)
>4XMA_1|Chain A|Sialidase B|Streptococcus pneumoniae serotype 4 TIGR4 (170187)
>2LLT_1|Chains A, B|Protein S100-A1|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 \(w=f(c)\)
3CWC , Knot 160 383 0.82 40 194 358 
SNAMKIVIAPDSYKESLSALEVATAIEQGFREIWPDADYLKLPLADGGEGTVEAMVEATAGRIVHVEVTGPLGHRVNAFYGLSGDARSAFIEMAAASGLEQVPPAQRDPLKTTSWGTGELIRHALDAGVEHIIIGIGGSATNDGGAGMVQALGARLRDAQGNDIAQGGIGLETLASIDISGLDKRLSACHIEVACDVTNPLTGKEGASAVFGPQKGATPEMIERLDTALTRYAHLIARDLHVDVLDLAGGGAAGGMGAALYAFCGAQLRRGIEIVTDALHLEACLADADLVITGEGRIDSQTIHGKVPIGVANIAKRYNKPVIGIAGSLTADVSVVHEHGLDAVFSVIYTICTLEDALKNASENVRMTARNVAATLKAGQQLR
4XMA , Knot 256 658 0.84 40 261 596 
ISPIFQGGSYQLNNKSIDISSLLLDKLSGESQTVVMKFKADKPNSLQALFGLSNSKAGFKNNYFSIFMRDSGEIGVEIRDAQKGINYLFSRPASLWGKHKGQAVENTLVFVSDSKDKTYTMYVNGIEVFSETVDTFLPISNINGIDKATLGAVNREGKEHYLAKGSIDEISLFNKAISDQEVSTIPLSNPFQLIFQSGDSTQANYFRIPTLYTLSSGRVLSSIDARYGGTHDSKSKINIATSYSDDNGKTWSEPIFAMKFNDYEEQLVYWPRDNKLKNSQISGSASFIDSSIVEDKKSGKTILLADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDNDFRYTVRENGVVYNETTNKPTNYTINDKYEVLEGGKSLTVEQYSVDFDSGSLRERHNGKQVPMNVFYKDSLFKVTPTNYIAMTTSQNRGESWEQFKLLPPFLGEKHNGTYLCPGQGLALGSSNRLIFATYTSGELTYLISDDSGQTWKKSSASIPFKNATAEAQMVELRDGVIRTFFRTTTGKIAYMTSRDSGETWSKVSYIDGIQQTSYGTQVSAIKYSQLIDGKEAVILSTPNSRSGRKGGQLVVGLVNKEDDSIDWKYHYGIDLPSYGYAYSAITELPNHHIGVLFEKYDSWSRNELHLSNVVQYIDLEINDLT
2LLT , Knot 49 93 0.79 36 74 89 
GSELETAMETLINVFHAHSGKEGDKYKLSKKELKELLQTELSGFLDAQKDVDAVDKVMKELDENGDGEVDFQEYVVLVAALTVACNNFFWENS

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 \(c\).

\(|P_{f(3CWC_1)}(2) \setminus P_{f(4XMA_1)}(2)|=40\), \(|P_{f(4XMA_1)}(2) \setminus P_{f(3CWC_1)}(2)|=107\). 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 1:00110111110000001011011011001100111010010111101101010111010110110101011110010110110101001110111101100111100011000011010110011011100111111101000111111011110100101001101111100110101011000101001011001001101001101111100110101100100110001011100101011011111111111111011011010011011001101010110101110101010000101011111101100000111111101010101100011011101100100100110010001010100111010110010
Pair \(Z_2\) Length of longest common subsequence
3CWC_1,4XMA_1 147 5
3CWC_1,2LLT_1 174 4
4XMA_1,2LLT_1 211 4

Newick tree

 
[
	2LLT_1:10.27,
	[
		3CWC_1:73.5,4XMA_1:73.5
	]:29.77
]

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 \((0.85)(0.8)(\frac{1041 }{\log_{20} 1041}-\frac{383}{\log_{20}383})=174.\)
Status Protein1 Protein2 d d1/2
Query variables 3CWC_1 4XMA_1 218 170.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]