CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4GNI_1 5KMK_1 7MYT_1 Letter Amino acid
28 21 7 E Glutamic acid
35 16 36 S Serine
23 23 10 R Arginine
21 29 21 G Glycine
26 11 21 T Threonine
12 11 9 Y Tyrosine
53 24 15 A Alanine
27 15 8 D Aspartic acid
13 18 10 H Histidine
27 14 10 I Isoleucine
21 12 15 K Lycine
18 17 15 P Proline
0 6 10 W Tryptophan
17 5 11 N Asparagine
0 7 5 C Cysteine
10 18 13 Q Glutamine
33 36 24 L Leucine
3 9 3 M Methionine
14 13 10 F Phenylalanine
28 24 21 V Valine 

4GNI_1|Chains A, B|Putative heat shock protein|Chaetomium thermophilum var. thermophilum DSM 1495 (759272)
>5KMK_1|Chain A|High affinity nerve growth factor receptor|Homo sapiens (9606)
>7MYT_1|Chains A, C[auth H]|B25.M05 Fab Heavy 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 \(w=f(c)\)
4GNI , Knot 170 409 0.83 36 203 373 
MAESASKAAPGERVVIGITFGNSNSSIAHTVDDKAEVIANEDGDRQIPTILSYVDGDEYYGQQAKNFLVRNPKNTVAYFRDILGQDFKSVDPTHNHASAHPQEAGDNVVFTIKDKAEEDAEPSTLTVSEIATRYLRRLVGAASEYLGKKVTSAVITIPTNFTEKQKAALIAAAAAADLEVLQLISEPAAAVLAYDARPEATISDKIIVVADLGGSRSDVTVLASRSGMYTILATVHDYEYHGIALDKVLIDHFSKEFLKKNPGAKDPRENPRSLAKLRLEAESTKRALSRSTNASFSVESLIDGLDFASTINRLRYETIARTVFEGFNRLVESAVKKAGLDPLDVDEVIMSGGTSNTPRIAANFRYIFPESTRILAPSTDPSALNPSELQARGAALQASLIQEHHHHHH
5KMK , Knot 145 329 0.85 40 207 315 
SSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLGHHHHHH
7MYT , Knot 120 274 0.82 40 175 259 
MKHLWFFLLLVAAPRWVLSQVQLQQWGAGLLKPSETLSLTCAVNGGSFSIYYWSWIRQPPGKGLDWIGEINQSGSTNYNPSLKSRVTMSVDTSKSQFSLRMTSVTAADTAIYYCARAPRIRWGSYRLKQTNFDSWGQGTLVTVFNQIKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTSGRHHHHHHGLNDIFEAQKIEWHE

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 \(c\).

\(|P_{f(4GNI_1)}(2) \setminus P_{f(5KMK_1)}(2)|=76\), \(|P_{f(5KMK_1)}(2) \setminus P_{f(4GNI_1)}(2)|=80\). 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 1:1100100111100111110110000011001000101110001000110110010100001001001110010001101001110010010100001010100110011101000100010100101001100010011111000110010011101100100000111111111101011011001111111001010101000111110111000010111000110011101000000111100111001000110001110010001001101010100000110000010101001101101100100100001100110110011001100111011010011101100001011101001110000111100010110100101011110101100000000
Pair \(Z_2\) Length of longest common subsequence
4GNI_1,5KMK_1 156 6
4GNI_1,7MYT_1 170 6
5KMK_1,7MYT_1 180 6

Newick tree

 
[
	7MYT_1:90.49,
	[
		4GNI_1:78,5KMK_1:78
	]:12.49
]

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 \((0.85)(0.8)(\frac{738 }{\log_{20} 738}-\frac{329}{\log_{20}329})=112.\)
Status Protein1 Protein2 d d1/2
Query variables 4GNI_1 5KMK_1 140 127.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]