CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5FYI_1 4CKH_1 1OMW_1 Letter Amino acid
24 27 39 S Serine
23 15 23 T Threonine
19 35 42 R Arginine
31 38 60 E Glutamic acid
27 51 77 L Leucine
12 6 24 M Methionine
23 15 36 F Phenylalanine
21 13 31 P Proline
8 4 7 W Tryptophan
27 20 56 K Lycine
17 24 37 V Valine
23 34 38 A Alanine
15 6 17 N Asparagine
16 17 40 D Aspartic acid
5 7 15 C Cysteine
11 23 32 Q Glutamine
20 8 32 I Isoleucine
23 23 40 G Glycine
15 10 21 H Histidine
21 6 22 Y Tyrosine 

5FYI_1|Chains A, B|LYSINE-SPECIFIC DEMETHYLASE 4A|HOMO SAPIENS (9606)
>4CKH_1|Chains A, B, C, D|ARF-GAP WITH COILED-COIL, ANK REPEAT AND PH DOMAIN-CONTAINING PROTEIN 1|HOMO SAPIENS (9606)
>1OMW_1|Chain A|G-protein coupled receptor kinase 2|Bos taurus (9913)
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 \(w=f(c)\)
5FYI , Knot 167 381 0.86 40 238 367 
MHHHHHHSSGVDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
4CKH , Knot 155 382 0.80 40 193 356 
GPLGSMTVKLDFEECLKDSPRFRASIELVEAEVSELETRLEKLLKLGTGLLESGRHYLAASRAFVVGICDLARLGPPEPMMAECLEKFTVSLNHKLDSHAELLDATQHTLQQQIQTLVKEGLRGFREARRDFWRGAESLEAALTHNAEVPRRRAQEAEEAGAALRTARAGYRGRALDYALQINVIEDKRKFDIMEFVLRLVEAQATHFQQGHEELSRLSQYRKELGAQLHQLVLNSAREKRDMEQRHVLLKQKELGGEEPEPSLREGPGGLVMEGHLFKRASNAFKTWSRRWFTIQSNQLVYQKKYKDPVTVVVDDLRLCTVKLCPDSERRFCFEVVSTSKSCLLQADSERLLQLWVSAVQSSIASAFSQARLDDSPRGPGQ
1OMW , Knot 265 689 0.83 40 285 640 
MADLEAVLADVSYLMAMEKSKATPAARASKKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLKHLEEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMKELLACSHPFSKSAIEHVQGHLVKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARKKTKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLLTMEEIQSVEETQIKERKCLLLKIRGGKQFVLQCDSDPELVQWKKELRDAYREAQQLVQRVPKMKNKPRAPVVELSKVPLIQRGSANGL

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 \(c\).

\(|P_{f(5FYI_1)}(2) \setminus P_{f(4CKH_1)}(2)|=106\), \(|P_{f(4CKH_1)}(2) \setminus P_{f(5FYI_1)}(2)|=61\). 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 1:100000000110110001010011000001010101101010100100100011010001100111101111001010100001001111111001101001110000100011010010011000000010000100100001001010111011010101000010010110100110110000110101100101011110001110000101001001011010010011100100100110111110100001110001011011110001111001000110111011010011100110010000110001100100111000000110101011100101000011011000011000110101101100001
Pair \(Z_2\) Length of longest common subsequence
5FYI_1,4CKH_1 167 3
5FYI_1,1OMW_1 157 4
4CKH_1,1OMW_1 168 4

Newick tree

 
[
	4CKH_1:85.42,
	[
		5FYI_1:78.5,1OMW_1:78.5
	]:6.92
]

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 \((0.85)(0.8)(\frac{763 }{\log_{20} 763}-\frac{381}{\log_{20}381})=103.\)
Status Protein1 Protein2 d d1/2
Query variables 5FYI_1 4CKH_1 136 131
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]