CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6UUL_1 5GZH_1 5AHY_1 Letter Amino acid
7 17 3 Q Glutamine
2 15 9 M Methionine
5 16 10 W Tryptophan
7 5 2 C Cysteine
17 25 1 K Lycine
16 20 6 P Proline
27 22 30 V Valine
11 32 37 A Alanine
23 41 21 G Glycine
15 35 37 L Leucine
7 18 10 F Phenylalanine
29 33 21 S Serine
11 31 7 Y Tyrosine
19 16 17 T Threonine
7 13 11 R Arginine
6 24 4 N Asparagine
11 20 8 D Aspartic acid
6 27 6 E Glutamic acid
4 21 7 H Histidine
5 18 14 I Isoleucine 

6UUL_1|Chains A, C|D5 Fab Heavy Chain|Homo sapiens (9606)
>5GZH_1|Chains A, B|Endo-beta-1,2-glucanase|Chitinophaga pinensis (strain ATCC 43595 / DSM 2588 / NCIB 11800 / UQM 2034) (485918)
>5AHY_1|Chain A|HALORHODOPSIN|HALOBACTERIUM SALINARUM (2242)
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 \(w=f(c)\)
6UUL , Knot 105 235 0.81 40 155 224 
QVQLVQSGAEVKKPGSSVTISCKPVGGTFTNFAIHWVRQAPGQGLEWVGGRVPVVGIYKYGKKFHDRLRLYEDDPMKTVFLELRSLTSDDTGVYYCTRWRGCGMCPYDTSSYYNDASDVWGPGTKVIVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK
5GZH , Knot 187 449 0.84 40 255 426 
MMSCGGSSSHQSTKDSTATDTLALSADSIFNIVEEQTFQYFWDGAEPVSGMARERYHVDGNYPENDMNVVTSGGSGFGVMALLVGIERGYISREQGLERLMKIVSFLEKADRFHGAWPHWLYGETGKVKPFGQKDNGGDLVETSFMIQGLLCVRQYFANGNEQEKALAARIDQLWKAVEFSWYRNGKNVLYWHWSPNYKWQMNFPVTGYNECLIMYILAAASPTHGIPAEVYHEGWAKSGAIKDSINAYGHTLKLSHNFAKEYGGPLFWSHYSYLGLDPHGLKDRYADYWENNLNHVLINREWCIQNPKHYKGYGPDSWGLTASYSVKGYAAHAPGENNDLGVISPTAALSSMPYTPEYSKQAMVHWYNDMRTKIFGKYGFYDAFSETENWYPQQYLAIDQGPIVVMMENYRSGLLWKLFMSCPEVQAGLKKLDFQSPYLKLEHHHHHH
5AHY , Knot 111 261 0.78 40 149 239 
AAAVRENALLSSSLWVNVALAGIAILVFVYMGRTIRPGRPRLIWGATLMIPLVSISSYLGLLSGLTVGMIEMPAGHALAGEMVRSQWGRYLTWALSTPMILLALGLLADVDLGSLFTVIAADIGMCVTGLAAAMTTSALLFRWAFYAISCAFFVVVLSALVTDWAASASSAGTAEIFDTLRVLTVVLWLGYPIVWAVGVEGLALVQSVGVTSWAYSVLDVFAKYVFAFILLRWVANNERTVAVAGQTLGTMSSDDHHHHHH

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 \(c\).

\(|P_{f(6UUL_1)}(2) \setminus P_{f(5GZH_1)}(2)|=49\), \(|P_{f(5GZH_1)}(2) \setminus P_{f(6UUL_1)}(2)|=149\). 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 1:0101100110100110010100011110100111011001110110111101111110001001000101000011001110100100000110000010101101000000000100111110011101100011011111100000011011110110001101101010011100110011111000110010011011000110000100100010000100010100000
Pair \(Z_2\) Length of longest common subsequence
6UUL_1,5GZH_1 198 4
6UUL_1,5AHY_1 158 4
5GZH_1,5AHY_1 196 6

Newick tree

 
[
	5GZH_1:10.19,
	[
		6UUL_1:79,5AHY_1:79
	]:25.19
]

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 \((0.85)(0.8)(\frac{684 }{\log_{20} 684}-\frac{235}{\log_{20}235})=125.\)
Status Protein1 Protein2 d d1/2
Query variables 6UUL_1 5GZH_1 160 120
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]