CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7GJF_1 6KQO_1 6KOE_1 Letter Amino acid
17 32 41 A Alanine
26 29 56 G Glycine
29 29 59 L Leucine
17 11 66 F Phenylalanine
24 10 41 T Threonine
3 5 22 W Tryptophan
12 1 4 C Cysteine
16 14 41 S Serine
11 12 17 R Arginine
21 9 26 N Asparagine
9 30 20 E Glutamic acid
13 11 27 P Proline
27 29 42 V Valine
17 17 15 D Aspartic acid
14 10 9 Q Glutamine
7 4 20 H Histidine
11 23 59 I Isoleucine
11 29 24 K Lycine
10 10 38 M Methionine
11 18 28 Y Tyrosine 

7GJF_1|Chains A, B|3C-like proteinase|Severe acute respiratory syndrome coronavirus 2 (2697049)
>6KQO_1|Chains A, B, C, D, E, F, G, H, I, J, K, L|Ketol-acid reductoisomerase|Saccharolobus solfataricus (2287)
>6KOE_1|Chains A, H[auth E]|AA3-600 quinol oxidase subunit I|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 \(w=f(c)\)
7GJF , Knot 134 306 0.83 40 196 290 
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ
6KQO , Knot 141 333 0.82 40 191 309 
MDKTVLDANLDPLKGKTIGVIGYGNQGRVQATIMRENGLNVIVGNVKDKYYELAKKEGFEVYEIDEAVRRSDVALLLIPDEVMKEVYEKKIAPVLQGKKEFVLDFASGYNVAFGLIRPPKSVDTIMVAPRMVGEGIMDLHKQGKGYPVLLGVKQDASGKAWDYAKAIAKGIGAIPGGIAVISSFEEEALLDLMSEHTWVPILFGAIKACYDIAVKEYGVSPEAALLEFYASGELAEIARLIAEEGIFNQMVHHSTTSQYGTLTRMFKYYDVVRRIVENEAKYIWDGSFAKEWSLEQQAGYPVFYRLWELATQSEMAKAEKELYKLLGRKVKND
6KOE , Knot 252 655 0.83 40 269 587 
MKFKWDEFFVTGDPLILGAQVSIALSTIAIIFVLTYFKKWKWLWSEWITTVDHKKLGIMYIISAVIMLFRGGVDGLMMRAQLALPNNSFLDSNHYNEIFTTHGTIMIIFMAMPFLIGLINVVVPLQIGARDVAFPYLNNLSFWTFFVGAMLFNISFVIGGSPNAGWTSYMPLASNDMSPGPGENYYLLGLQIAGIGTLMTGINFMVTILKMRTKGMTLMRMPMFTWTTLITMVIIVFAFPVLTVALALLSFDRLFGAHFFTLEAGGMPMLWANLFWIWGHPEVYIVILPAFGIFSEIISSFARKQLFGYKAMVGSIIAISVLSFLVWTHHFFTMGNSASVNSFFSITTMAISIPTGVKIFNWLFTMYKGRISFTTPMLWALAFIPNFVIGGVTGVMLAMAAADYQYHNTYFLVSHFHYVLIAGTVFACFAGFIFWYPKMFGHKLNERIGKWFFWIFMIGFNICFFPQYFLGLQGMPRRIYTYGPNDGWTTLNFISTVGAFMMGVGFLILCYNIYYSFRYSTREISGDSWGVGRTLDWATSSAIPPHYNFAVLPEVKSQDAFLHMKEEKTELYPESKFKKIHMPSNSGRPFFMSVAFGLAGFGLVFEWYWMGVVGLIGVLLCMVLRSFEYDNGYYISVDEIKETERKISEHHHHHH

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 \(c\).

\(|P_{f(7GJF_1)}(2) \setminus P_{f(6KQO_1)}(2)|=89\), \(|P_{f(6KQO_1)}(2) \setminus P_{f(7GJF_1)}(2)|=84\). 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 1:011001111010101011010010001011110011001001100000110100001110000001110110101011100100011010100101001000110101100101110001010110001101010101011010010111010000101001001011011011001010101111000010111000010101111101111010011100100010010111100000110000101111101001111101010100110011010011101110001011011000011010
Pair \(Z_2\) Length of longest common subsequence
7GJF_1,6KQO_1 173 4
7GJF_1,6KOE_1 195 4
6KQO_1,6KOE_1 162 5

Newick tree

 
[
	7GJF_1:95.59,
	[
		6KQO_1:81,6KOE_1:81
	]:14.59
]

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 \((0.85)(0.8)(\frac{639 }{\log_{20} 639}-\frac{306}{\log_{20}306})=92.5\)
Status Protein1 Protein2 d d1/2
Query variables 7GJF_1 6KQO_1 117 112
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]