CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6LBJ_1 8KFY_1 3GBV_1 Letter Amino acid
14 26 19 D Aspartic acid
23 18 12 R Arginine
8 10 5 C Cysteine
17 6 17 H Histidine
16 26 24 I Isoleucine
48 27 26 L Leucine
6 9 7 M Methionine
24 19 14 V Valine
15 16 16 N Asparagine
20 13 16 Q Glutamine
15 17 16 G Glycine
17 19 17 F Phenylalanine
16 21 15 T Threonine
4 3 1 W Tryptophan
19 31 17 A Alanine
25 30 14 K Lycine
19 4 12 P Proline
29 18 18 S Serine
10 13 17 Y Tyrosine
23 28 21 E Glutamic acid 

6LBJ_1|Chains A, B|Poly(A) RNA polymerase GLD2|Mus musculus (10090)
>8KFY_1|Chain A|Guanine nucleotide-binding protein G(i) subunit alpha-1|Homo sapiens (9606)
>3GBV_1|Chains A, B|Putative LacI-family transcriptional regulator|Bacteroides fragilis (272559)
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 \(w=f(c)\)
6LBJ , Knot 161 368 0.86 40 215 350 
MGSSHHHHHHSSGLEVLFQGPHMGGSEPREITLPEAKDKLSQQILELFETCQQQASDLKKKELCRAQLQREIQLLFPQSRLFLVGSSLNGFGARSSAGDLCLVVKEEPCFFQVNQKTEARHILTLVHKHFCTRLSGYIERPQLIRAKVPIVKFRDKVSCVEFALNVNNTVGIRNTFLLRTYAYLENRVRPLVLVIKKWASHHDINDASRGTLSSYSLVLMVLHYLQTLPEPILPSLQKIYPESFSTSVQLHLVHHAPCNVPPYLSKNESSLGDLLLGFLKYYATEFDWNTQMISVREAKAIPRPDDMEWRNKYICVEEPFDGTNTARAVHEKQKFDMIKDQFLKSWQRLKNKRDLNSVLPLRAATLKR
8KFY , Knot 153 354 0.84 40 203 334 
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF
3GBV , Knot 134 304 0.84 40 192 291 
MSLASNKKYTFACLLPKHLEGEYWTDVQKGIREAVTTYSDFNISANITHYDPYDYNSFVATSQAVIEEQPDGVMFAPTVPQYTKGFTDALNELGIPYIYIDSQIKDAPPLAFFGQNSHQSGYFAARMLMLLAVNDREIVIFRKIHEGVIGSNQQESREIGFRQYMQEHHPACNILELNLHADLNIEDSRMLDDFFREHPDVKHGITFNSKVYIIGEYLQQRRKSDFSLIGYDLLERNVTCLKEGTVSFLIAQQPELQGFNSIKTLCDHLIFRKEVACTNYMPIDLLTKENIDYYHSEGHHHHHH

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 \(c\).

\(|P_{f(6LBJ_1)}(2) \setminus P_{f(8KFY_1)}(2)|=92\), \(|P_{f(8KFY_1)}(2) \setminus P_{f(6LBJ_1)}(2)|=80\). 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 1:11000000000011011101101110010010110100010001101100000010010000100101000101111000111110010111100011010111000101101000001001101100010001010100101101011110100010010111010001110001110001010001011111100110000100100101000011111100100110111101001010010001010110011001110100000011011111100010010100011010010111010010100001010011010001011000001011000110010010000010011110110100
Pair \(Z_2\) Length of longest common subsequence
6LBJ_1,8KFY_1 172 4
6LBJ_1,3GBV_1 169 6
8KFY_1,3GBV_1 167 3

Newick tree

 
[
	6LBJ_1:85.82,
	[
		3GBV_1:83.5,8KFY_1:83.5
	]:2.32
]

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 \((0.85)(0.8)(\frac{722 }{\log_{20} 722}-\frac{354}{\log_{20}354})=100.\)
Status Protein1 Protein2 d d1/2
Query variables 6LBJ_1 8KFY_1 128 125.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]