CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6XBF_1 1HDX_1 8UKE_1 Letter Amino acid
9 11 10 R Arginine
10 12 9 N Asparagine
15 39 15 V Valine
10 7 6 M Methionine
9 16 6 F Phenylalanine
16 24 10 T Threonine
4 6 16 Y Tyrosine
36 31 17 A Alanine
13 22 16 I Isoleucine
8 32 13 K Lycine
13 21 15 S Serine
4 2 2 W Tryptophan
12 6 4 Q Glutamine
17 29 31 L Leucine
13 20 10 P Proline
25 38 13 G Glycine
10 7 7 H Histidine
17 17 14 D Aspartic acid
1 15 1 C Cysteine
6 19 24 E Glutamic acid 

6XBF_1|Chains A, C[auth B], E[auth C], G[auth D]|BlaNDM-4_1_JQ348841|Klebsiella pneumoniae (573)
>1HDX_1|Chains A, B|ALCOHOL DEHYDROGENASE|Homo sapiens (9606)
>8UKE_1|Chains A, B, C, D, E, F|Norbelladine 4'-O-methyltransferase|Narcissus aff. pseudonarcissus MK-2014 (1540222)
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 \(w=f(c)\)
6XBF , Knot 113 248 0.83 40 168 239 
GSHMMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR
1HDX , Knot 159 374 0.84 40 204 359 
STAGKVIKCKAAVLWEVKKPFSIEDVEVAPPKAYEVRIKMVAVGICRTDDHVVSGNLVTPLPVILGHEAAGIVESVGEGVTTVKPGDKVIPLFTPQCGKCRVCKNPESNYCLKNDLGNPRGTLQDGTRRFTCRGKPIHHFLGTSTFSQYTVVDENAVAKIDAASPLEKVCLIGCGFSTGYGSAVNVAKVTPGSTCAVFGLGGVGLSAVMGCKAAGAARIIAVDINKDKFAKAKELGATECINPQDYKKPIQEVLKEMTDGGVDFSFEVIGRLDTMMASLLCCHEACGTSVIVGVPPASQNLSINPMLLLTGRTWKGAVYGGFKSKEGIPKLVADFMAKKFSLDALITHVLPFEKINEGFDLLHSGKSIRTVLTF
8UKE , Knot 110 239 0.84 40 160 229 
MGASIDDYSLVHKNILHSEDLLKYILETSAYPREHPQLKELREVTEKHEWSSMLVPADEGLFLSMLLKLMNAKRTIEIGVYTGYSLLTTALALPEDGKITAIDVNKSYYEIGLPFIQKAGVEHKINFIESEALPVLDQMLEEMKEEDLYDYAFVDADKSNYANYHERLVKLVRIGGAILYDNTLWYGSVAYPEYPGLHPEEEVARLSFRNLNTFLAADPRVEISQVSIGDGVTICRRLY

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 \(c\).

\(|P_{f(6XBF_1)}(2) \setminus P_{f(1HDX_1)}(2)|=70\), \(|P_{f(1HDX_1)}(2) \setminus P_{f(6XBF_1)}(2)|=106\). 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 1:10011110101011001001000110111001110110000010111111110011110011011110011000001011011000101111111100100001111011011111001011000111001111100010111011101101101111011011110000010111010011111011000010011011010000011010111111101011110001100011100010110010
Pair \(Z_2\) Length of longest common subsequence
6XBF_1,1HDX_1 176 4
6XBF_1,8UKE_1 174 3
1HDX_1,8UKE_1 150 3

Newick tree

 
[
	6XBF_1:91.28,
	[
		8UKE_1:75,1HDX_1:75
	]:16.28
]

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 \((0.85)(0.8)(\frac{622 }{\log_{20} 622}-\frac{248}{\log_{20}248})=105.\)
Status Protein1 Protein2 d d1/2
Query variables 6XBF_1 1HDX_1 135 112.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]