CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7ZVL_1 6VDP_1 2GMU_1 Letter Amino acid
33 8 30 I Isoleucine
61 37 35 L Leucine
31 8 24 F Phenylalanine
44 29 11 P Proline
36 30 12 R Arginine
31 5 25 N Asparagine
26 15 11 Q Glutamine
33 36 27 G Glycine
31 15 23 T Threonine
14 6 4 W Tryptophan
41 24 25 V Valine
14 5 9 M Methionine
42 66 18 A Alanine
35 22 25 D Aspartic acid
47 21 25 E Glutamic acid
18 9 8 H Histidine
31 3 31 K Lycine
12 4 5 C Cysteine
42 18 25 S Serine
23 4 17 Y Tyrosine 

7ZVL_1|Chain A|Protein arginine N-methyltransferase 5|Homo sapiens (9606)
>6VDP_1|Chain A|3-methyl-L-tyrosine peroxygenase|Streptomyces lavendulae (1914)
>2GMU_1|Chains A, B|Putative pyridoxamine 5-phosphate-dependent dehydrase, WbdK|Escherichia coli O55:H7 (244320)
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 \(w=f(c)\)
7ZVL , Knot 252 645 0.84 40 287 604 
MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
6VDP , Knot 143 365 0.77 40 175 316 
MTAPADTVHPAGQPDYVAQVATVPFRLGRPEELPGTLDELRAAVSARAGEAVRGLNRPGARTDLAALLAATERTRAALAPVGAGPVGDDPSESEANRDNDLAFGIVRTRGPVAELLVDAALAALAGILEVAVDRGSDLEDAAWQRFIGGFDALLGWLADPHSAPRPATVPGAGPAGPPVHQDALRRWVRGHHVFMVLAQGCALATACLRDSAARGDLPGAEASAAAAEALMRGCQGALLYAGDANREQYNEQIRPTLMPPVAPPKMSGLHWRDHEVLIKELAGSRDAWEWLSAQGSERPATFRAALAETYDSHIGVCGHFVGDQSPSLLAAQGSTRSAVGVIGQFRKIRLSALPEQPATQQGEPS
2GMU , Knot 166 390 0.84 40 222 367 
GHMINYPLASSTWDDLEYKAIQSVLDSKMFTMGEYVKQYETQFAKTFGSKYAVMVSSGSTANLLMIAALFFTKKPRLKKGDEIIVPAVSWSTTYYPLQQYGLRVKFVDIDINTLNIDIESLKEAVTDSTKAILTVNLLGNPNNFDEINKIIGGRDIILLEDNCESMGATFNNKCAGTFGLMGTFSSFYSHHIATMEGGCIVTDDEEIYHILLCIRAHGWTRNLPKKNKVTGVKSDDQFEESFKFVLPGYNVRPLEMSGAIGIEQLKKLPRFISVRRKNAEYFLDKFKDHPYLDVQQETGESSWFGFSFIIKKDSGVIRKQLVENLNSAGIECRPIVTGNFLKNTDVLKYFDYTVHNNVDNAEYLDKNGLFVGNHQIELFDEIDYLREVLK

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 \(c\).

\(|P_{f(7ZVL_1)}(2) \setminus P_{f(6VDP_1)}(2)|=148\), \(|P_{f(6VDP_1)}(2) \setminus P_{f(7ZVL_1)}(2)|=36\). 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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
Pair \(Z_2\) Length of longest common subsequence
7ZVL_1,6VDP_1 184 4
7ZVL_1,2GMU_1 169 4
6VDP_1,2GMU_1 179 3

Newick tree

 
[
	6VDP_1:92.75,
	[
		7ZVL_1:84.5,2GMU_1:84.5
	]:8.25
]

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 \((0.85)(0.8)(\frac{1010 }{\log_{20} 1010}-\frac{365}{\log_{20}365})=171.\)
Status Protein1 Protein2 d d1/2
Query variables 7ZVL_1 6VDP_1 225 170.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]