CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5AZX_1 2KVE_1 2AQH_1 Letter Amino acid
1 1 8 N Asparagine
8 7 15 D Aspartic acid
8 4 11 E Glutamic acid
5 0 7 F Phenylalanine
0 1 4 W Tryptophan
5 0 5 H Histidine
8 12 9 K Lycine
2 2 10 M Methionine
2 2 13 P Proline
8 3 13 T Threonine
3 3 6 Y Tyrosine
5 2 18 V Valine
7 5 36 A Alanine
2 2 1 C Cysteine
11 3 28 G Glycine
7 4 19 I Isoleucine
6 3 16 S Serine
4 3 13 R Arginine
2 1 10 Q Glutamine
9 7 27 L Leucine 

5AZX_1|Chains A, B, C, D|Transmembrane emp24 domain-containing protein 10|Rattus norvegicus (10116)
>2KVE_1|Chain A|Mesencephalic astrocyte-derived neurotrophic factor|Homo sapiens (9606)
>2AQH_1|Chain A|Enoyl-[acyl-carrier-protein] reductase [NADH]|Mycobacterium tuberculosis (1773)
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 \(w=f(c)\)
5AZX , Knot 54 103 0.81 38 86 100 
GSISFHLPVNSRKCLREEIHKDLLVTGAYEITDQSGGAGGLRTHLKITDSAGHILYAKEDATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEA
2KVE , Knot 36 65 0.77 36 56 62 
MGKYDKQIDLSTVDLKKLRVKELKKILDDWGETCKGCAEKSDYIRKINELMPKYAPKAASARTDL
2AQH , Knot 114 269 0.79 40 167 253 
MTGLLDGKRILVSGIITDSSVAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL

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 \(c\).

\(|P_{f(5AZX_1)}(2) \setminus P_{f(2KVE_1)}(2)|=70\), \(|P_{f(2KVE_1)}(2) \setminus P_{f(5AZX_1)}(2)|=40\). 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 1:1010101110000010001000111011001000011111100010100011011010001001011100000011010100010101100111101001101
Pair \(Z_2\) Length of longest common subsequence
5AZX_1,2KVE_1 110 3
5AZX_1,2AQH_1 151 4
2KVE_1,2AQH_1 161 3

Newick tree

 
[
	2AQH_1:84.33,
	[
		5AZX_1:55,2KVE_1:55
	]:29.33
]

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 \((0.85)(0.8)(\frac{168 }{\log_{20} 168}-\frac{65}{\log_{20}65})=35.0\)
Status Protein1 Protein2 d d1/2
Query variables 5AZX_1 2KVE_1 45 36
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]