CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
3JRA_1 8BAR_1 2IVI_1 Letter Amino acid
8 19 19 N Asparagine
4 13 18 E Glutamic acid
12 18 25 L Leucine
6 9 15 T Threonine
0 2 5 W Tryptophan
4 13 20 Y Tyrosine
5 13 28 A Alanine
10 8 17 Q Glutamine
5 6 19 G Glycine
0 6 10 H Histidine
10 8 22 V Valine
6 11 12 R Arginine
2 11 16 F Phenylalanine
6 12 24 D Aspartic acid
1 16 15 I Isoleucine
7 8 20 K Lycine
6 4 4 M Methionine
2 10 20 P Proline
4 17 20 S Serine
0 4 2 C Cysteine 

3JRA_1|Chains A, B|DNA-binding protein fis|Escherichia coli (83333)
>8BAR_1|Chain A|E. coli C7 DarT1|Escherichia coli (562)
>2IVI_1|Chain A[auth B]|ISOPENICILLIN N SYNTHETASE|Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (227321)
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 \(w=f(c)\)
3JRA , Knot 52 98 0.81 34 82 95 
MFEQRVNSDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN
8BAR , Knot 99 208 0.84 40 152 202 
SMTIQEIIQQRNIRSLFHFTHSDNLTSILDNGLMSRSELDNENNEYNCNDEERIDGHPDAICLSVSYPNAKMFYKYRCLKPGDWVILEINPSVLWAKDCAFYPTNAASNNVRFINLDLMKGAEAFSALFSENVFGIQRDVNLPSEYTTDVQAAILVFEKIPPSYIISTFHPNKESAEHFKRLYPQTIQRYYDNLNARTLYSQRHYYLG
2IVI , Knot 149 331 0.87 40 206 319 
MGSVSKANVPKIDVSPLFGDDQAAKMRVAQQIDAASRDTGFFYAVNHGINVQRLSQKTKEFHMSITPEEKWDLAIRAYNKEHQDQVRAGYYLSIPGKKAVESFCYLNPNFTPDHPRIQAKTPTHEVNVWPDETKHPGFQDFAEQYYWDVFGLSSALLKGYALALGKEENFFARHFKPDDTLASVVLIRYPYLDPYPEAAIKTAADGTKLSFEWHEDVSLITVLYQSNVQNLQVETAAGYQDIEADDTGYLINCGSYMAHLTNNYYKAPIHRVKWVNAERQSLPFFVNLGYDSVIDPFDPREPNGKSDREPLSYGDYLQNGLVSLINKNGQT

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 \(c\).

\(|P_{f(3JRA_1)}(2) \setminus P_{f(8BAR_1)}(2)|=48\), \(|P_{f(8BAR_1)}(2) \setminus P_{f(3JRA_1)}(2)|=118\). 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 1:11000100011010010000010001100010011000110101001001001111010011101110000100001111111001010001000110
Pair \(Z_2\) Length of longest common subsequence
3JRA_1,8BAR_1 166 3
3JRA_1,2IVI_1 182 4
8BAR_1,2IVI_1 162 3

Newick tree

 
[
	3JRA_1:89.02,
	[
		8BAR_1:81,2IVI_1:81
	]:8.02
]

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 \((0.85)(0.8)(\frac{306 }{\log_{20} 306}-\frac{98}{\log_{20}98})=65.3\)
Status Protein1 Protein2 d d1/2
Query variables 3JRA_1 8BAR_1 84 61.5
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]