CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3UCG_1 5VRC_1 8YKA_1 Letter Amino acid
2 1 12 C Cysteine
7 14 67 E Glutamic acid
5 10 46 K Lycine
3 15 42 P Proline
7 16 35 S Serine
7 30 62 A Alanine
1 10 24 Q Glutamine
4 14 30 T Threonine
3 11 11 Y Tyrosine
1 7 19 M Methionine
3 4 30 N Asparagine
5 21 55 D Aspartic acid
9 16 50 G Glycine
6 11 59 I Isoleucine
5 30 68 L Leucine
7 22 58 R Arginine
3 16 10 H Histidine
5 11 31 F Phenylalanine
0 5 3 W Tryptophan
6 16 52 V Valine 

3UCG_1|Chain A|Polyadenylate-binding protein 2|Homo sapiens (9606)
>5VRC_1|Chains A, B, C, D|Bifunctional coenzyme PQQ synthesis protein C/D|Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (272630)
>8YKA_1|Chains A, B, C, D, E, F|Transitional endoplasmic reticulum ATPase|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 \(w=f(c)\)
3UCG , Knot 49 89 0.82 38 79 87 
GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGI
5VRC , Knot 124 280 0.83 40 170 265 
MGSSHHHHHHSSGLVPRGSHMTAQFPPPVPDTEQRLLSHEELEAALRDIGARRYHNLHPFHRLLHDGKLSKDQVRAWALNRYYYQAMIPVKDAALLARLPDAQLRRIWRQRIVDHDGDHEGDGGIERWLKLAEGVGFTRDYVLSTKGILSATRFSVDAYVHFVSERSLLEAIASSLTEMFSPTIISERVAGMLKNYDFITKDTLAYFDKRLTQAPRDADFALDYVKRHATTPEMQRAAIDALTFKCNVLWTQLDALYFAYVAPGMVPPDAWQPGEGLVAE
8YKA , Knot 282 764 0.81 40 276 674 
LSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPS

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 \(c\).

\(|P_{f(3UCG_1)}(2) \setminus P_{f(5VRC_1)}(2)|=33\), \(|P_{f(5VRC_1)}(2) \setminus P_{f(3UCG_1)}(2)|=124\). 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 1:11010100101101001101001010101010100101100010101011101010000010001110001101001011100000111
Pair \(Z_2\) Length of longest common subsequence
3UCG_1,5VRC_1 157 5
3UCG_1,8YKA_1 211 4
5VRC_1,8YKA_1 192 4

Newick tree

 
[
	8YKA_1:10.28,
	[
		3UCG_1:78.5,5VRC_1:78.5
	]:28.78
]

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 \((0.85)(0.8)(\frac{369 }{\log_{20} 369}-\frac{89}{\log_{20}89})=86.7\)
Status Protein1 Protein2 d d1/2
Query variables 3UCG_1 5VRC_1 107 70
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]

Graphviz Engine:
Graphviz Engine: