CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
7KXG_1 4FSF_1 6YJA_1 Letter Amino acid
26 25 7 K Lycine
0 5 0 W Tryptophan
17 49 14 V Valine
25 43 17 L Leucine
8 15 7 F Phenylalanine
12 15 2 Y Tyrosine
5 24 6 Q Glutamine
24 51 10 G Glycine
30 26 14 I Isoleucine
18 28 5 S Serine
17 28 8 T Threonine
25 60 5 A Alanine
8 39 6 R Arginine
17 21 10 N Asparagine
13 24 7 D Aspartic acid
7 0 1 C Cysteine
24 26 12 E Glutamic acid
13 13 5 H Histidine
8 12 7 M Methionine
13 32 4 P Proline 

7KXG_1|Chains A, B, C, D, E, F|4-hydroxy-tetrahydrodipicolinate synthase|Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (192222)
>4FSF_1|Chain A|Penicillin-binding protein 3|Pseudomonas aeruginosa (287)
>6YJA_1|Chains A, B|CBS domain-containing protein YkuL|Bacillus subtilis (strain 168) (224308)
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 \(w=f(c)\)
7KXG , Knot 133 310 0.82 38 180 298 
MRGSHHHHHHGSMDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF
4FSF , Knot 213 536 0.83 38 231 502 
HHHHHHARSVRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPTATEQQQVNAAPAKGGRG
6YJA , Knot 73 147 0.82 38 113 143 
MISLQSDQLLEATVGQFMIEADKVAHVQVGNNLEHALLVLTKTGYTAIPVLDPSYRLHGLIGTNMIMNSIFGLERIEFEKLDQITVEEVMLTDIPRLHINDPIMKGFGMVINNGFVCVENDEQVFEGIFTRRVVLKELNKHIRSLNK

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 \(c\).

\(|P_{f(7KXG_1)}(2) \setminus P_{f(4FSF_1)}(2)|=47\), \(|P_{f(4FSF_1)}(2) \setminus P_{f(7KXG_1)}(2)|=98\). 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 1:1010000000101000111111011101100101000001011000100110111111001001010000000010111000010010111111001000111110110001101110111000010001100000111001011111001110010010000110110000010110010101000101110010111101001100111001101110100011101101100111000000100100010010011100001111001101111100101011100100001101001100001011
Pair \(Z_2\) Length of longest common subsequence
7KXG_1,4FSF_1 145 6
7KXG_1,6YJA_1 161 4
4FSF_1,6YJA_1 162 3

Newick tree

 
[
	6YJA_1:83.31,
	[
		7KXG_1:72.5,4FSF_1:72.5
	]:10.81
]

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 \((0.85)(0.8)(\frac{846 }{\log_{20} 846}-\frac{310}{\log_{20}310})=145.\)
Status Protein1 Protein2 d d1/2
Query variables 7KXG_1 4FSF_1 186 145
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]