CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
4AYO_1 3HHS_1 6QFE_1 Letter Amino acid
52 46 11 A Alanine
14 17 9 H Histidine
17 31 12 K Lycine
15 45 17 P Proline
14 10 5 W Tryptophan
21 26 7 Y Tyrosine
30 49 13 R Arginine
11 40 10 N Asparagine
34 47 11 D Aspartic acid
16 27 15 Q Glutamine
10 22 4 M Methionine
24 45 19 S Serine
24 48 3 E Glutamic acid
27 33 10 T Threonine
23 40 16 V Valine
4 8 12 C Cysteine
33 30 19 G Glycine
14 38 10 I Isoleucine
45 56 19 L Leucine
19 36 5 F Phenylalanine 

4AYO_1|Chain A|MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE|CAULOBACTER SP. (366602)
>3HHS_1|Chain A|Phenoloxidase subunit 2|Manduca sexta (7130)
>6QFE_1|Chains A, B|Kallikrein-5|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 \(w=f(c)\)
4AYO , Knot 180 447 0.82 40 225 420 
MASETTPEDWKALAADVRSEFQWAWQGYVAKAWGKDEINPVSGTSRSFFIEGHDLGLSLVEALDTLWIMGLDAEFQAGVDWVKANLSFDVDGNAQVFETNIRLVGGLLSAHLASGDPVLLAKARDLADRLAKAFEASPHGLPWRYVNLRTGAVSDPETNLAEIGTYLSEFGVLSQLTGERKYFDMAKRAMRHTLDRRSKIGLMAANIHAMTGAFTSRNASIDVYADSFYEYLWDAWALFGDEDCKRWAVECVDAQLAHQAKRYDGRLWFPMVDFETGAVTGTAQSELAAYYAGLLGQVGRKAQGDDYLASFTYLQATFGVIPESIDVTTGQPRRKHTGLRPEYPDACLNLWLIDRDPRYRRLAAIHYREMKATSRAAFGYTALKDITTRPMTQDDNCPGYWWSEQMKYYYLLFSDTPRIDYGQLQLSTEANVLRGFRKVLEHHHHHH
3HHS , Knot 273 694 0.85 40 298 649 
ADIFDSFELLYDRPGEPMINTKGEDKVLFELTEQFLTPEYANNGLELNNRFGDEEEVSRKIILKNLDKIPEFPKAKQLPNDADFSLFLPSHQEMANEVIDVLMSVTENQLQELLSTCVYARINLNPQLFNYCYTVAIMHRRDTGKVRVQNYAEIFPAKFLDSQVFTQAREAAAVIPKTIPRTPIIIPRDYTATDLEEEHRLAYWREDLGINLHHWHWHLVYPFSASDEKIVAKDRRGELFFYMHQQIIARYNCERLCNSLKRVKKFSDWREPIPEAYYPKLDSLTSARGWPPRQAGMRWQDLKRPVDGLNVTIDDMERYRRNIEEAIATGNVILPDKSTKKLDIDMLGNMMEASVLSPNRDLYGSIHNNMHSFSAYMHDPEHRYLESFGVIADEATTMRDPFFYRVHAWVDDIFQSFKEAPHNVRPYSRSQLENPGVQVTSVAVESAGGQQNVLNTFWMQSDVNLSKGLDFSDRGPVYARFTHLNHRPFRYVIKANNTASARRTTVRIFIAPKTDERNLPWALSDQRKMFIEMDRFVVPLSAGENTITRQSTESSLTIPFEQTFRDLSIQGSDPRRSELAAFNYCGCGWPQHMLVPKGTVGGVAYQLFVMLSNYELDKIEQPDGRELSCVEASMFCGLKDKKYPDARPMGYPFDRPSNSATNIEDFSAMSNMGLQDIVIKLSDVTEPNPRNPPA
6QFE , Knot 108 227 0.86 40 167 221 
IINGSDCDMHTQPWQAALLLRPNQLYCGAVLVHPQWLLTAAHCRKKVFRVRLGHYSLSPVYESGQQMFQGVKSIPHPGYSHPGHSNDLMLIKLNRRIRPTKDVRPINVSSHCPSAGTKCLVSGWGTTKSPQVHFPKVLQCLNISVLSQKRCEDAYPRQIDDTMFCAGDKAGRDSCQGDSGGPVVCNGSLQGLVSWGDYPCARPNRPGVYTNLCKFTKWIQETIQANS

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 \(c\).

\(|P_{f(4AYO_1)}(2) \setminus P_{f(3HHS_1)}(2)|=43\), \(|P_{f(3HHS_1)}(2) \setminus P_{f(4AYO_1)}(2)|=116\). 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 1:110000100101111010001011101011011100010110100001110100111011011001111110101011101101010101010101100010111111010110101111101001100110110101011110010100111001000110110010011110010100001011001100010000011111101011011100001010101001000110111111000000111001010110010000101111110100111010100011100111110110010100011010010101111100101001010000011010010101011110001000011110000101000111100110010001100000011011000100001110001010010101000101101100110000000
Pair \(Z_2\) Length of longest common subsequence
4AYO_1,3HHS_1 159 5
4AYO_1,6QFE_1 188 4
3HHS_1,6QFE_1 203 4

Newick tree

 
[
	6QFE_1:10.20,
	[
		4AYO_1:79.5,3HHS_1:79.5
	]:23.70
]

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 \((0.85)(0.8)(\frac{1141 }{\log_{20} 1141}-\frac{447}{\log_{20}447})=180.\)
Status Protein1 Protein2 d d1/2
Query variables 4AYO_1 3HHS_1 228 186
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]