CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6DBZ_1 8XBC_1 5GGV_1 Letter Amino acid
8 17 6 N Asparagine
4 11 2 H Histidine
6 19 7 I Isoleucine
11 23 14 V Valine
12 21 34 S Serine
7 14 18 T Threonine
7 54 13 A Alanine
6 7 6 R Arginine
4 25 10 D Aspartic acid
13 33 15 L Leucine
9 29 9 F Phenylalanine
11 14 12 P Proline
2 10 11 Y Tyrosine
4 10 2 W Tryptophan
2 0 5 C Cysteine
1 25 15 Q Glutamine
16 29 9 E Glutamic acid
15 44 12 G Glycine
8 31 13 K Lycine
4 13 1 M Methionine 

6DBZ_1|Chains A, B|Nudix hydrolase 1|Arabidopsis thaliana (3702)
>8XBC_1|Chain A|XylA|Vibrio sp. EA2 (3079860)
>5GGV_1|Chain A[auth L]|light chain|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 \(w=f(c)\)
6DBZ , Knot 73 150 0.81 40 116 147 
GSHMSTGEAIPRVAVVVFILNGNSILLGRRRSSIGNSTFALPGGHLEFGESFEECAAREVMEETGLKIEKMKLLTVTNNVFKEAPTPSHYVSVSIRAVLVDPSQEPKNMEPEKCEGWDWYDWENLPKPLFWPLEKLFGSGFNPFTHGGGD
8XBC , Knot 175 429 0.82 38 213 389 
MLRNHKLSKVFSATAISLFLSSTAFADTTVRMMHIETDPNVLGVWEEIAKDFEAKNPDIKVNLEFLENEAFKAKLPTLLQSQQKPDLFYSWGGGNFQVRAESGLLEDMEGYSATLNQELSAAGMNAFKIDGKQYGAPYMVSQVGFWYNKKLFKQAGIDGESIQTWDEFLTAIEKLKAAGITPIAVGGADKWPMHFYWSYLAMRAGGQEAFAAAMQDQGDGFAGEAFVRAGEELKRLAALEPFQPGFMAAGYGESAGLFGDYKAAIHLMGDWDYNFQAQQAVDKKGVVDSDLGFMNFPVLKGGAGAGSDTLGGINGFAFAKGAKPEAAKWLEFFLNENSQTKLAEIDQIIPVAKGADKGLKNPFKQKISQTISSAQWHQVFFDQALGADVGGVVNDISVGIVNGDVTPKEAAEQVQEAWEMRLEHHHHHH
5GGV , Knot 99 214 0.82 40 149 200 
DIQMTQSPSSLSASVGDRVTITCRASQSINSYLDWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYSTPFTFGPGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 \(c\).

\(|P_{f(6DBZ_1)}(2) \setminus P_{f(8XBC_1)}(2)|=40\), \(|P_{f(8XBC_1)}(2) \setminus P_{f(6DBZ_1)}(2)|=137\). 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 1:100100101110111111110100111100000110001111110101100100011001100011010010110100011001101000101010111101000100101000011010010011011111100111011011001110
Pair \(Z_2\) Length of longest common subsequence
6DBZ_1,8XBC_1 177 3
6DBZ_1,5GGV_1 155 3
8XBC_1,5GGV_1 172 4

Newick tree

 
[
	8XBC_1:90.27,
	[
		6DBZ_1:77.5,5GGV_1:77.5
	]:12.77
]

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 \((0.85)(0.8)(\frac{579 }{\log_{20} 579}-\frac{150}{\log_{20}150})=124.\)
Status Protein1 Protein2 d d1/2
Query variables 6DBZ_1 8XBC_1 157 105
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]