CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
6NVH_1 7QDX_1 3IRA_1 Letter Amino acid
11 9 7 F Phenylalanine
22 18 11 P Proline
16 33 9 S Serine
14 15 5 H Histidine
10 35 16 I Isoleucine
10 15 7 M Methionine
8 14 6 Q Glutamine
19 38 21 E Glutamic acid
8 10 6 Y Tyrosine
21 34 7 R Arginine
17 23 6 D Aspartic acid
7 5 3 C Cysteine
7 11 8 N Asparagine
21 56 10 G Glycine
5 0 5 W Tryptophan
7 30 7 T Threonine
25 43 8 V Valine
22 54 9 A Alanine
36 39 10 L Leucine
14 25 12 K Lycine 

6NVH_1|Chain A|Fibroblast growth factor receptor 4|Homo sapiens (9606)
>7QDX_1|Chains A, B|Inosine-5'-monophosphate dehydrogenase|Escherichia coli (562)
>3IRA_1|Chain A|Conserved protein|Methanosarcina mazei (192952)
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 \(w=f(c)\)
6NVH , Knot 133 300 0.84 40 192 284 
MVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDRVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSHHHHHH
7QDX , Knot 196 507 0.80 38 223 457 
MGSSHHHHHHSSGLVPRGSHMLRIAKEALTFDDVLLVPAHSTVLPNTADLSTQLTKTIRLNIPMLSAAMDTVTEARLAIALAQEGGIGFIHKNMSIERQAEEVRRVKKHESAIVRDPVTVTPSTKIIELLQMAREYGFSGFPVVEQGELVGIVTGRDLRVKPNAGDTVAAIMTPKDKLVTAREGTPLEEMKAKLYENRIEKMLVVDENFYLRGLVTFRDIEKAERKPNACKDEQGRLRVGAAVGAGAGNEERVDALVAAGVDVLLIDSSHGHSEGVLQRIRETRAKYPDLQIIGGNVATAAGARALAEAGCSAVKVGIGPGSICTTRIVTGVGVPQITAVADAVEALEGTGIPVIADGGIRFSGDIAKAIAAGASAVMVGSMLAGTEESPGEIELYQGRSYKSYRGMGSLGAMSKGSSDRYFQSDNAADKLVPEGIEGRVAYKGRLKEIIHQQMGGLRSCMGLTGCGTIDELRTKAEFVRISGAGIQESHVHDVTITKESPNYRLGS
3IRA , Knot 86 173 0.85 40 141 167 
AEPNRLIKEKSPYLLQHAYNPVDWYPWGEEAFEKARKENKPVFLSIGYSTCHWCHMMAHESFEDEEVAGLMNEAFVSIKVDREERPDIDNIYMTVCQIILGRGGWPLNIIMTPGKKPFFAGTYIPKNTRFNQIGMLELVPRIKEIWEQQHEEVLDSAEKITSTIQEMIKESSG

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 \(c\).

\(|P_{f(6NVH_1)}(2) \setminus P_{f(7QDX_1)}(2)|=65\), \(|P_{f(7QDX_1)}(2) \setminus P_{f(6NVH_1)}(2)|=96\). 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 1:110101110111011000111101110101101101011110110100100111011000100001101100101101110000110111100001110111001101010011010011100011101111100100110110010000010001110011100001101101111011001000000001011101111011100100000011011111101101110101111100110110010010011001101011100010111000101001101100111110000000
Pair \(Z_2\) Length of longest common subsequence
6NVH_1,7QDX_1 161 7
6NVH_1,3IRA_1 197 3
7QDX_1,3IRA_1 180 4

Newick tree

 
[
	3IRA_1:98.52,
	[
		6NVH_1:80.5,7QDX_1:80.5
	]:18.02
]

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 \((0.85)(0.8)(\frac{807 }{\log_{20} 807}-\frac{300}{\log_{20}300})=138.\)
Status Protein1 Protein2 d d1/2
Query variables 6NVH_1 7QDX_1 170 136.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]