CoV2D BrowserTM

CoV2D project home | Random page
Parikh vectors
5EJC_1 5ZJC_1 2DBW_1 Letter Amino acid
16 17 25 D Aspartic acid
22 8 28 K Lycine
5 4 2 W Tryptophan
15 9 9 R Arginine
19 6 21 E Glutamic acid
11 13 19 I Isoleucine
8 8 11 M Methionine
13 9 12 F Phenylalanine
16 12 23 P Proline
9 4 15 Y Tyrosine
22 15 23 V Valine
5 10 17 N Asparagine
8 24 33 G Glycine
8 9 5 H Histidine
7 1 0 C Cysteine
9 12 15 Q Glutamine
36 17 25 L Leucine
21 12 21 S Serine
9 16 16 T Threonine
17 36 46 A Alanine 

5EJC_1|Chains A, B|TBC1 domain family member 7|Homo sapiens (9606)
>5ZJC_1|Chain A|Metallo-beta-lactamase type 2|Klebsiella pneumoniae (573)
>2DBW_1|Chains A, C|Gamma-glutamyltranspeptidase|Escherichia coli K12 (83333)
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 \(w=f(c)\)
5EJC , Knot 121 276 0.82 40 176 260 
GFRGVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVWKVLLGILPPHHESHAKVMMYRKEQYLDVLHALKVVRFVSDATPQAEVYLRMYQLESGKLPRSPSFPLEPDDEVFLAIAKAMEEMVEDSVDCYWITRRFVNQLNTKYRDSLPQLPKAFEQYLNLEDGRLLTHLRMCSAAPKLPYDLWFKRCFAGCLPESSLQRVWDKVVSGSCKILVFVAVEILLTFKIKVMALNSAEKITKFLENIPQDSSDAIVSKAIDLWHKHCGTPVHSS
5ZJC , Knot 111 242 0.84 40 165 234 
GEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR
2DBW , Knot 152 366 0.81 38 208 350 
AAPPAPPVSYGVEEDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYESNQ

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 \(c\).

\(|P_{f(5EJC_1)}(2) \setminus P_{f(5ZJC_1)}(2)|=87\), \(|P_{f(5ZJC_1)}(2) \setminus P_{f(5EJC_1)}(2)|=76\). 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 1:110110000010111000010000100100011110100111101111111100000101110000001011011011011001010101010100100101100101110100011111101100110001000110001100100000001101101100010100101100101001110110011100011101100010011001101000111111101110101011110010010011001100000111001101100001011000
Pair \(Z_2\) Length of longest common subsequence
5EJC_1,5ZJC_1 163 3
5EJC_1,2DBW_1 164 4
5ZJC_1,2DBW_1 157 4

Newick tree

 
[
	5EJC_1:82.80,
	[
		5ZJC_1:78.5,2DBW_1:78.5
	]:4.30
]

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 \((0.85)(0.8)(\frac{518 }{\log_{20} 518}-\frac{242}{\log_{20}242})=79.0\)
Status Protein1 Protein2 d d1/2
Query variables 5EJC_1 5ZJC_1 97 92
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)],
\[ \delta= \alpha \mathrm{min} + (1-\alpha) \mathrm{max}= \begin{cases} d &\alpha=0,\\ d_1/2 &\alpha=1/2 \end{cases} \]