CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
2DLF_1 6SCP_1 9BXZ_1 Letter Amino acid
10 5 33 G Glycine
1 3 27 M Methionine
6 6 39 F Phenylalanine
18 9 49 S Serine
6 2 17 P Proline
1 0 3 W Tryptophan
4 1 42 Y Tyrosine
9 9 41 V Valine
2 10 47 A Alanine
5 8 28 R Arginine
2 1 6 C Cysteine
3 1 16 H Histidine
8 3 35 T Threonine
6 3 25 Q Glutamine
4 6 44 I Isoleucine
11 7 50 L Leucine
6 2 59 K Lycine
4 1 42 N Asparagine
4 6 48 D Aspartic acid
3 7 49 E Glutamic acid 

2DLF_1|Chain A[auth L]|PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)-KAPPA (LIGHT CHAIN))|Mus musculus (10090)
>6SCP_1|Chains A, B|Cell division protein SepF|Corynebacterium glutamicum ATCC 13032 (196627)
>9BXZ_1|Chains A, B|Ribonucleoside-diphosphate reductase subunit alpha|Bacillus subtilis (1423)
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 \(w=f(c)\)
2DLF , Knot 56 113 0.78 40 88 104 
DVVMTQTPLSLPVSLGNQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLEIKR
6SCP , Knot 47 90 0.78 38 74 87 
MSYQSTIVPVELHSFEDAQVIGGAFRDGDAVVFDMSLLSREEARRIVDFAAGLCFALRGKMQKIDSVTFAVVPELSNISTSELERAARIR
9BXZ , Knot 271 700 0.84 40 286 659 
MSQNQVPKWIQLNNEIMIQKDGKFQFDKDKEAVHSYFVDYINQNTVFFHNLKEKLDYLVENQYYEEEFLSLYSFEDIKEVFKTAYAKKFRFPSFMSAFKFYNDYALKTNDKKKILERYEDRISIVALFFANGDTEKAKEYVNLMINQEYQPSTPTFLNAGRKRRGELVSCFLLEVNDSLNDISRAIDISMQLSKLGGGVSLNLSKLRAKGEAIKDVENATKGVVGVMKLLDNAFRYADQMGQRQGSGAAYLNIFHRDINDFLDTKKISADEDVRVKTLSIGVVIPDKFVELAREDKAAYVFYPHTIYKEYGQHMDEMDMNEMYDKFVDNPRVKKEKINPRKLLEKLAMLRSESGYPYIMFQDNVNKVHANNHISKVKFSNLCSEVLQASQVSSYTDYDEEDEIGLDISCNLGSLNILNVMEHKSIEKTVKLATDSLTHVSETTDIRNAPAVRRANKAMKSIGLGAMNLHGYLAQNGIAYESPEARDFANTFFMMVNFYSIQRSAEIAKEKGETFDQYEGSTYATGEYFDKYVSTDFSPKYEKIANLFEGMHIPTTEDWKKLKAFVAEHGMYHSYRLCIAPTGSISYVQSSTASVMPIMERIEERTYGNSKTYYPMPGLASNNWFFYKEAYDMDMFKVVDMIATIQQHIDQGISFTLFLKDTMTTRDLNRIDLYAHHRGIKTIYYARTKDTGQDSCLSCVV

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 \(c\).

\(|P_{f(2DLF_1)}(2) \setminus P_{f(6SCP_1)}(2)|=67\), \(|P_{f(6SCP_1)}(2) \setminus P_{f(2DLF_1)}(2)|=53\). 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 1:01110001101110110010100000001100010001010100110010111001000101110010101010010101001010011101000000111011010010100
Pair \(Z_2\) Length of longest common subsequence
2DLF_1,6SCP_1 120 3
2DLF_1,9BXZ_1 228 3
6SCP_1,9BXZ_1 222 4

Newick tree

 
[
	9BXZ_1:12.21,
	[
		2DLF_1:60,6SCP_1:60
	]:65.21
]

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 \((0.85)(0.8)(\frac{203 }{\log_{20} 203}-\frac{90}{\log_{20}90})=37.0\)
Status Protein1 Protein2 d d1/2
Query variables 2DLF_1 6SCP_1 43 39.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]