CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6HMB_1 7TFS_1 2FOZ_1 Letter Amino acid
25 14 21 D Aspartic acid
20 9 8 H Histidine
36 20 37 L Leucine
16 11 12 P Proline
23 4 18 R Arginine
16 4 18 Q Glutamine
5 1 1 W Tryptophan
17 25 30 G Glycine
19 8 11 I Isoleucine
27 11 12 K Lycine
10 6 9 M Methionine
9 26 15 T Threonine
21 17 31 S Serine
23 1 14 Y Tyrosine
24 12 21 V Valine
20 26 38 A Alanine
16 17 6 N Asparagine
2 8 6 C Cysteine
22 4 26 E Glutamic acid
13 8 13 F Phenylalanine 

6HMB_1|Chain A|Casein kinase II subunit alpha'|Homo sapiens (9606)
>7TFS_1|Chain A|Cytochrome c|Geobacter sulfurreducens (35554)
>2FOZ_1|Chain A|ADP-ribosylhydrolase like 2|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 \(w=f(c)\)
6HMB , Knot 155 364 0.83 40 212 344 
MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
7TFS , Knot 105 232 0.82 40 147 221 
MRSEVKIGLALTALLVAVTAAGAASIKNTKHDLSSGSTGATFKATNTDQICVFCHTPHNAQQDIPLWNRGNPTASTFTLYSSSSMNNVPVKQGFTADSISLFCMSCHDGATGLGGAVHNDPNGAAIAMVGGNDLITGEANLGTDLSNDHPVNFEVTPAGIAADGNLGALDTGTNPPTMKTGDVTNGLPLFKSARGATTLECGSCHKVHDNTDAPFLRTTMAGSKLCLGCHKK
2FOZ , Knot 144 347 0.81 40 185 328 
MASLSRFRGCLAGALLGDCVGSFYEAHDTVDLTSVLRHVQSLEPDPGTPGSERTEALYYTDDTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRGYGAGVVTVFKKLLNPKCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYSSVQDVQKFARLSAQLTHASSLGYNGAILQALAVHLALQGESSSEHFLKQLLGHMEDLEGDAQSVLDARELGMEERPYSSRLKKIGELLDQASVTREEVVSELGNGIAAFESVPTAIYCFLRCMEPDPEIPSAFNSLQRTLIYSISLGGDTDTIATMAGAIAGAYYGMDQVPESWQQSCEGYEETDILAQSLHRVFQKS

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 \(c\).

\(|P_{f(6HMB_1)}(2) \setminus P_{f(7TFS_1)}(2)|=124\), \(|P_{f(7TFS_1)}(2) \setminus P_{f(6HMB_1)}(2)|=59\). 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 1:1100000000000111111110010101010010000010001011011000000110011010000110110100000111011011000010001011001011001101100100110001111100100001001001100101010100110110000001110001010011100000010110111101001100001011000101101110001000010110110111011100011101000000110110111000101010000101010100111000000100110000001101011011001100000001010011001010111000001010011100110110
Pair \(Z_2\) Length of longest common subsequence
6HMB_1,7TFS_1 183 4
6HMB_1,2FOZ_1 173 4
7TFS_1,2FOZ_1 164 4

Newick tree

 
[
	6HMB_1:91.25,
	[
		2FOZ_1:82,7TFS_1:82
	]:9.25
]

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 \((0.85)(0.8)(\frac{596 }{\log_{20} 596}-\frac{232}{\log_{20}232})=103.\)
Status Protein1 Protein2 d d1/2
Query variables 6HMB_1 7TFS_1 130 105
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]